Well, ok, as said before, if you use the complex mode, you need:
a) rompaths...for each system one unique one....simply drag'n drop them in the rompath window in settings
b) assigned system default paths...since cmpro needs an indicator which rompath belongs to which system.
both a and b only have to be done only once (unless new systems are added).
The auto-assign button can help you to do b). And b) is done simply to NOT check where to put or fix a file during scan/rebuild every single time.
The action behind it looks in each rompath, checks the files and counts how many of them belongs to which software list. The winner is assigned. If no winner is found (e.g. if you don't have any files at all), the 1st rompath is assigned. In the end you need to ensure that each software lists is assigned to one distinct rompath. So you can't have let's say C64 files together with let's say Apple II files in one path. They need to be separated....which is pretty obvious, isn't it.
Most likely the basic mode with one profile per software list is easier for you to use....there you don't have to care about system default paths at all....and the batcher can actually auto create the rompaths for you, too.