If it helps, here's what I do........
Add the lights and run registration only, no stacking.
Note the sub with the highest score, so this can be used as the reference frame. I rename this file and copy it to it's own location, so I can use it with Ha, OIII subs, etc. Registration needs to be run again after renaming.
I also check all the other scores, so when stacking, un-tick anything below 300 before stacking, or if I'm using it for a luminance layer will un-tick anything below 1600 as I want the detail to be as sharp as possible.
In the other tabs, I add the subs from each night, each to its own tab. You can re-use the calibration frames for each tab if needed, by copying them to separate folder locations. DSS looks at the complete path, not just the file name to decide if a file is the same as a previous one already loaded.
If the calibration frames are in the first tab, they will affect all other frames regardless of which tab they are in. If they are in another tab, then they only affect that tab. So I put calibration frames into each of the other tabs and just leave the reference frame in the first.
If the reference frame is from Ha and I'm stacking OIII for instance, then make sure the reference frame is un-ticked before stacking.
John