Many people feel a bit daunted by LRGB imaging prefering the apparent simplicity of one shot colour imaging. This is a great shame since LRGB has some significant benefits - greater sensitivity, resolution not affected by a bayer matrix, more suited to narrow band imaging and an ability to do an unbinned luminence for detail and binned colour images. With this primer I am hoping to take some of the mystery out of LRGB and demonstrate the routines I have picked up which seem to work pretty well.
Notes on image capture
Filters
If your light pollution is quite low then a simple IR block filter is all you need for luminence. If light pollution is severely restricting your exposure time by producing excessive sky glow then use a light pollution filter - a CLS filter is a good choice and blocks IR. The trouble with light pollution filters is that the do require increased exposure time so only use if really necessary. My light pollution is significantly worse to the east then the west. If I am imaging near the zenith or to the west I can manage with just an IR blocking filter.
Choice of filters can be as complex an issue as you want to make it, and as expensive as well. I have found the series 2 Astronomik LRGB filter set to give good performance. They are also very tough and stand up to vigorous cleaning very well. Baader make a significantly cheaper set which represents good value for money. They let through marginally less light so may require slightly longer exposures. I don't know how tough they are compared with Astronomik.
Filter wheels
My first LRGB images were using a fastar system which meant I had to change filters manually. This is a real pain, the camera inevitably has a slightly different rotation on each image and getting condensation on the filters is another problem. The situation is much improved by use of a manual filter wheel, so long as you can remember which filter you have put where and which way to move the wheel! A motorised filter wheel seems like a rather extravagant expense but transforms LRGB capture into every bit as simple a procedure as using a one shot colour camera. The great advantage of a motorised wheel is that you can set up an image sequence which builds up your LRGB image as the session goes on rather than doing all the luminence, then the red, then green, then blue. No longer do you have to say, "will capture some RGB on the next clear night" Atik have now produced a motorised wheel for around £160 which will soon have a bolt on which will give USB connectivity. The total price is likely to be under £200. This might sound a lot but is a major undercutting of the price of currently available wheels.
Having said all that, you can get by quite happily with a manual wheel!
Exposure times
Many people believe that the luminance component is the most important so should be given the most time. The problem with this is that if the colour channels are given less exposure than the luminance colour saturation is poor leading to watery images. You can get around this by boosting colour saturation during processing but this introduces a lot of noise into the image. To avoid this each colour channel must be given as much exposure as the luminence. This sounds horrendous, an hour of luminence potentially needs 4 hours to become an RGB, no wonder people advocate one shot colour!. Fortunately we can bin the colour channels. By combining pixels into blocks of 4 (2x2 binning) we quadruple the chips sensitivity at the expense of reducing resolution. So a 1 hour luminence now requires a total of 45 minutes to make an acceptable LRGB. Better still, addition of the colour data actually improves the signal to noise ratio. The RGB image adds colour hue and saturation to the luminence. It isn't adding detail so the reduced resolution isn't an issue.
Chips vary in their sensitivity to different colours, filters have there own transmission characteristics as do scope optics. Colour transmission is also affected by the atmosphere with blue being scattered more low down than near the zenith. Each imaging system will tend to produce it's own individual colour cast. When starting off it is quite reasonable to use the same exposure times for R G and B. The problem with this approach is that you will find that you have to tone down one colour and boost another, typically blue needs a boost. This increases noise and is inefficient since you are wasting exposure time in the most sensitive channel. This is also an issue with one shot colour but with LRGB we can do something about it. As you learn the characteristics of your set up you will get a feel for how much you need to adjust the colour channels to deliver a balanced result. Knowing this you can set different exposure times for each colour. My ratio is G:R:B 1 : 1 :1 : 1.4.
The "proper" way to work out the correct ratio is to image a G2V star (same colour profile as the sun) and work out what corrections are needed to make it white. Well, when I move to Arizona and have all the clear nights I can handle I'll get on and do that. An alternative is to take an LRGB daytime image through the scope you are using and use your eyes to judge the correct colour. This is ok for some but you are dependent on the quality of your colour vision, I've never bothered.
Processing
Align and combine each channel seperately then align (but don't combine) the combined channel images. The RGB images will be smaller than the luminence so resize now to match the luminence. I use maxim to do all this but there are plenty of other programs that are around to do all this for you.
Procsssing the luminence
Process in the normal way, stretch the histogram, remove gradients and artefacts, sharpen and reduce background noise. I normally leave star processing until I have brought the LRGB together.
Processig the RGB
This is were the fun starts!
I use photoshop, other programs may work slightly differently but I am sure most are capable of performing similar function. I am using an image of M33 taken this autumn.
Merge the RGB channels before processing

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I have opened the RGB (and the lum) and, from the channels palette have selected merge/RGB. This will only work if the images are grey scale. If they are RGB then change under image/mode to greyscale. Choose the appropriate image for each channel. It will ask you if you want to save the individual channels but there is no point so click no to declutter your screen.
Stretching the histogram and adjusting bias
When processing colour images there are 2 colour issues to deal with, bias and balance. The bias relates to discrepancies in back ground colouration. A typical UK colour image is affected by LP which affects background colouration. LP will have a smaller affect on overall colour balance.
We have to stretch the RGB image using iterative curves and levels. When you bring up levels you find that the black points on the histogram are different. By adjusting the black point for each channel individually you will correct the bias and end up with a neutral grey/black background sky. Here are a couple of screen shots comparing the blue and red histograms

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The curves stretch should be done using the RGB master channel but after each curves adjustment you need to adjust the levels in each individual channel.
Here is the stretched and bias corrected RGB

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Adjusting Colour Balance
Colour balance is a very subjective thing. Fiddling around with the sliders using the colour balance tool can be a frustrating experience and difficult to get "right". Fortunately there is a way of approaching this effectively, provided your image has a good mix of RGB. Bring up the histogram window and choose the colour option. This should then display the histograms for the individual channels. Have a look at each histogram and you will see that there is a point on the right hand side where the curve meets the base line. This is called the pseudo white point (it isn't the true white point because the apparent baseline is actually not quite the bottom of the histogram but is raised slightly be the contribution of the stars). If you rest your cursor over the pseudo white point you can see the brightness level in the information area above. In this image above the red was 120 green 105 and blue 88. The idea is to adjust these white points so that they match using the colour balance tool. PS makes this very easy. ctrl b for colour balance and make sure preserve luminosity is checked. Select highlights (very important because we are adjusting the brightest portions of the target). The blue needs boosting. As you do this you will see the blue histogram move over to the right. Adjust the colour levels until the white points are similar.

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The above images show before and after balancing
You can also see the combined histogram with the colours laid on top of each other, the histograms are now nicely balanced but the image is a bit wishy washy.
Increase saturation
The process of combining an RGB with a luminence tends to reduce the colour saturation of the image. Provided you have reasonable signal to noise ratio in your RGB you can get away with boosting the saturation. You have to be careful and watch out for the image becoming noisy, better a smooth image with weak colour than a strong colourful one. It is at this point that you will be glad of those binned subs! It is a bit of a judgement call. Oversaturate slightly, if you can get away with it. If, after combining with the luminance you find that the saturation doesn't look right, go back and try again. Don't be tempted to adjust the saturation of the combined image because you will add more noise.

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Now we have good colour balance and adequate saturation however looking that the image you may feel it needs some tweaking. M33 has lots of bright areas made up of young bright blue stars. Also it has red Ha areas. You will have your own ideas on how the image should look so you can now make tweaks to the colour balance to achieve your ideal colour.

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Reduce noise
Since the RGB isn't adding detail you should apply some quite heavy noise reduction. It is possible to get away with some global gaussian blurring but I prefer to use Noel's space noise reduction. I find this a bit heavy for normal use, preferring the deep sky noise reduction tool or doing it myself. but for an RGB it works very nicely.

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Don't be alarmed at this stage if the image looks a bit underwhelming. Remember it is a resized binned image with no luminence to back it up.
Combining the luminence and RGB

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This luminance image has been processed ready for combining. It's mode has to be changed to RGB by going to Image/mode and checking RGB.
Bring up the RGB, select, copy then select the luminence and paste. You will just see the RGB so don't be disappointed! Because I have done some cropping it is necessary to line the images up again despite having aligned them previously. Fortunately there will be no rotation so this is very easy. Change the blend mode to difference and select the move arrow from the tools palette. Click on the image and move around with the mouse. You can make fine adjustments with the cursor keys (make sure you have clicked on the image with the move arrow other wise you will just change the blend mode!). Once aligned the image looks like this

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Now comes the magical bit! To combine an RGB onto a luminence we just want to add the colour so change the blend mode to colour and hopefully an extraordinary transformation takes place. For me this step is the most exciting part of astroimaging! If you wanted to do it the other way around and add a luminence to an RGB you would use luminance as the blend mode.

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You can now make tweaks to the image in the seperate layers. Often you can see more clearly where a bit of extra sharpening would help. Noise may be creeping in from the RGB layer. You can flatten the image and make further adjustments to the whole image. I have just made a few tweaks to the stars including getting rid of some small blue halos.
here is the final image

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I have converted the Fits to tiffs and uploaded them to UK Astronomers so that you can download and have a play. The luminance has been deconvolved using CCDSharp and I have used digital development processing in maxim. It needs further stretching and removal of a few artefacts but not much else.
I hope this was useful. I would be grarteful for feedback or suggestions.