William,
If is best practice to do your flats by channel and not combined. The reason is that you may have dust on the filters that are not consistent across the range. To get the cleanest image, stack each flat channel set to create separate L, R, G & B master flats, then apply those in the Image Calibration routine as you pre-process each stack of lights.
If you are interested, I have a detailed workbook for PI that I share with others. If you are interested in my latest version, just drop me a line at jkmorse57@gmail.com and I will be happy to send it along, free of charge of course.
Best,
Jim