Essentially, you store all of your bias, dark and flat fields in a single location, and then use the Set Calibration dialog in MaxIM DL to manage your calibration files and, optionally, create masters. There are a number of options available in the dialog (feel free to ask specific questions) but little house keeping is required once your library is ‘up and running’ in MaxIM. There’s also a ‘calibration wizard’, but I’ve not used it.
Also, check out the MaxIM help topics under the Help menu. There’s a whole section on image calibration and the use of calibration groups in the ‘Processing Images’ section.