Hi,
For DSLR images I process each nights images up to and including the debayer process. Then use the script "SubFrameSelector" to find the best SNR and Eccentricity image for all the images. I guess you can use your predefine best image as the reference. I then continue to StarAlignment and add all the debayered images for various night and continue the pre-processing with LocalNormalization, ImageIntegration and sometime DrizzleIntegration.
I assume the process is very similar for CCD images, except there is no Debayer required.
Look up
John