Well, you can set up TD so it won't move players around for you. You could then manually award the prizes once the tournament is over (points and money, etc). However, the rankings would still be combined if you care about the rankings. If you only care about "stats" as far as money and/or points, the rankings wouldn't matter.
As far as I know, you cannot split tables into two separate tournaments within the program; you'll just have to work around it in some way.