If you look at the amount of players that sign after the 40th round, they're basically taking fliers on guys like Ricky Bowen and HS kids that are probably going to college.
In general, most teams have 5 rookie ball teams.
One team is for players that are more developed- ie college players (For example New York-Penn League)
One team is for players that are less developed- ie high school players, junior college players, a few college players that are somewhat raw, some Latinos. (Appalachain League)
One team is going to be based at their spring training facility and is for guys that are raw and long range projects, some Latinos. (AZL league)
One team will be based in the Dominican, and those teams are basically 16-17 year old kids. As they get older, they will progress and in 7-8 years when they are 23-24 they will be MLB ready if all goes well.
One team is based in Venezuela, and is a Venezuelan version of it's Dominican cousin.
So, you're talking about stocking 3 teams with draft picks. Just guessing, an average MLB team probably signs 30-35 picks a year give or take a few. I want to say a minor league roster is 25 players or so, and with the Latino players and free agents, who are guys that didn't get drafted at all, they should be able to reasonably stock their farm with 35 draft picks. And then there are a select few guys that are good enough to start out in A ball or AA, like Strasburg might do.