Looks like it'll go like this:
Step 1: NYCFC Youth Development League (U9, U10, U11): 11-Team intraleague competition with a focus on development and performance over winning. Top graduates move on to Step 2, but theoretically could leave and get picked up by another team.
Step 2: NCYFC Academy (U14, U16, U18): One team per age group, these players are officially part of the NYCFC machine and eligible to become homegrown players. They'll likely play in the NE division of this league:
http://en.wikipedia.org/wiki/U.S._Soccer_Development_Academy
*One article mentioned that academies will soon have a U12 division as well, which will bridge the gap between Step 1 and Step 2.
Step 3: NYCFC "Baby Blues" USL Pro: Become professional and either jump straight to the first team, or spend another year or two with the USL Pro squad developing.
Step 4: NYCFC: Bring home the MLS Cup for the organization you just spent 10+ years climbing the ladder with.