Best way to run it is Fantrax. Second best way is to have someone crazy enough to keep a google doc spread sheet up to date all the time.
Otherwise have some NA slots, open each roster up to 50 normal slots for the summer, and then say that they have to be down to 45 by whatever date you want to do your prospect draft, bringing you back up to 50, and then changing the settings back to 25 players and 25 prospects.