Patch - to answer your questions:
1) Yes. The only requirements are that only one team from each conference can play in an exempt event, and the same team can not play in the same event more than once in four years. This is one reason why the conferences host the tourneys -- it's the only chance they can keep the event going from year to year.
2). You are correct, in your team's case your RPI was hurt more by your in conference teams than your games against the biggies, but there is not much you can do about that in the short run. In fact, it may be one reason why the schedule was made -- to balance out the RPI Strength of Schedule. However, what I am saying is that your RPI may have been helped more if you replaced two out of three of the games scheduled against the top 50 with a few more quality but winnable away games, for example teams ranked 50-150 and won them. This is because the NCAA puts a premium on winning away games. The key is if you schedule that way you have to win the games (hence Siena's RPI). Now, if you were to win the away games against the top 50, that would be the ultimate - but I think we can agree that it would be tough to win 2 out 3 games in that scenario.
JG