Art;
The first thing I'd tell you is to wait on the roster that APujols is hoping to release very soon, see
Real World Rosters:: Read Inside.....
If you've been trying to use the Cubby07 beta, I'd forget it. I've been messing with it for a couple of days now and find it to be a mess. No defensive ratings and lots of duplicate players. It's really not worth your time.
As for setting the minor league's the way you want them, you can now simply delete any league you don't want and the players will become free agents. Go to the League Tools tab at the bottom and you'll find a couple of different avenues for deleting unwanted leagues.