They come from the USL2, so you could just dump new clubs (modelled after colleges) into the existing USL2 conferences, I think that's what most people do. If you didn't wanna build the rules then at least it would look the way you want in their history, news items about the draft, etc.
Yeah they're really not good at it, I tried different options in the editor to make them take advantage of the loan system more, but they're not great at this kind of squad management