if international, that would be "international" scouting budget related, methinks. if oyu don't have any int'l league enabled, you can zero out that budget. the created ones on july 2nd(defualt date) are just amatuers in that context.
an independent league may not allow affiliations? i've never enabled one, but that's my guess. so, getting players from there would require posting or some other method etc depending on your choice of settings.
also, if you want it to mimic a particular level of minor league, while choosing somethign other than a normal minor league expansion, i'd screenshot or take note of the PCM/sabermetric pcms, league totals etc... then atuo-calc the modifiers at least once on opening day or as you normally would over time.
you'd want to mimic anythign that could possibly influence development at that level. if you intend it to be affiliated with your ML teams, i'd strongly suggest just doing it the normal way. you may need to change your ML league region to <none specified> but you should be able to use MiL teams anywhere in the World dB. travel is inconsequential.. japan to iowa? no problem! what's an international dateline ootp?
if it's just a 2nd indenpendent league (not game settings vernacular), trial and error with abackup until you iron out the kinks. get creative do what you want.