I run a 14-team, contract keeper league. The contract part of it makes it a little easier to do the Minors thing. We get 5 minors players, and unlike normal leagues, any player can be placed in the Minors. The only catch is that they can only be put there during our Minors draft in the pre-season. So calling up your minors player is sort of like a one-way street.
Anyways, we can keep any player that hasn't exceeded the MLB rookie qualifications on the Minors Roster for free at the end of the season. If they surpass the MLB rookie qualification, then the player must be activated or the player will become an unrestricted free agent at the end of the year.
Hope that helped!