Commissioner mandate is essentially the only way to do it. But you don't want to spread the dates out as far as RonCo suggests. Free Agents sign quite quickly in OOTP2006. If you left 15 days between "offer dates", every player that received an offer on the first date would have signed by the second date, and there'd be no chance for negotiation.
The best way, as far as I can tell, is to mandate a FA period similiar to OOTP6: pick a week or two week period in the game (shortly after the FAs file and/or coinciding with the Winter Meetings seems like a good idea to me), and then sim one game day for every real world day for that period. Once that period is over, jump the game up to whatever the next event in your world is (Rule V, Spring Training, whatever). That way, people have an opportunity to bid competitively for the players, but it doesn't take up so much time that everyone gets incredibly bored of the process. Any FAs that haven't signed during your preset period will make up their minds as you jump forward in time once they realize no better offers are coming.
- Kai