I just wanted to chime in and say that one of the things I like about SGP is that it allows for quite a bit of personal preference on how to organize imaging several objects over multiple nights.
The process that I’ve settled on is to develop a single sequence file for a night’s shooting session that may have multiple objects, each possibly with several filters depending upon my wishes for that night. If I have several nights of imaging, I make a copy of the sequence file and use a different directory in which to place my light frames each night. I like to have my raw files separated by night.
If I need to disturb the optical train from one night to another I try to first obtain a set of flats to associate with prior light frames, proceed with the changes, and then associate new flats with the next set of light frames. When possible, I try not to change the optical train so that I can apply a single set of flats to light frames from all of my nights, however this is not always possible. By having separate directories for each night I find that I can organize all of this a little more easily.
My preference for file names is to use lots of information in the name: object name, filter, CCD temperature, date, etc. I also try to use a “suffix” number to distinguish one night’s set of files from another. This comes in handy when combining calibrated images from multiple nights/directories later. This can be a bit cumbersome and makes for lengthy file names, however it’s the system that works best for me. Much of this information is available in the FITS header, however I still like to have it in the file name for my convenience.
You have opportunity to adopt your own system, which will likely be refined as you go along and get used to using SGP. Have fun, and good luck!