Here is a website with suggested rules, including for a minor league draft: http://www.letsplay2.com/baseball/rules.cfm
My league's rules are very similar. We allow four roster spots for minor leaguers and have a 2-round draft each season after our main roster auction to restock it with any player that is still rookie eligible. We started with 3 minor league spots for a couple of seasons, but found it to be too restrictive. we also didn't want too many spots so there would always been some top level rookies available during the auction. The low number of spots makes it very risky to draft hot shot prospects still in A ball since they can sit in the minors for several more seasons before getting the call.
Other rules surrounding the minor leaguers are that they don't automatically have to be called up when they get to the big leagues as this website suggests. During the offseason if a minor leaguer plays the equivalent of 1/2 a season (350 AB's, 100 IP or 30 appearances) he becomes keeper eligible. Anything less than that the player can be kept without limits as a minor leaguer.
We allow players to be sent to our minor league roster as long as they have been sent down in real life. Also, we have a rule that any player picked up must be kept on the active roster for two weeks before being sent to the minors or DL to prevent those slots from being used to stash players directly from the waiver wire. This rule is extremely helpful when news breaks that a hot prospect is about to be called up so a team can't get a free, no-risk preview by stashing the player in their minors.