There used to be some provisions for player movement back and forth a la a "Reserves" side but now I don't believe there is any affiliation, except for a few of the teams (RBNY, DCU) that field youth teams in the Super-Y and Super-20 USL leagues.
The PDL and W-League, men's and women's respectively, are amateur leauges. Players in these leagues retain their NCAA college sports eligibility.