[andrewas]

Due to a lack of psychic abilities among ironworks members, it would help if you posted the specific mods you are downloading.

Speaking generaly, most mods should work with both BG2 and ToB installed. Some mods require ToB. The only mod I can immediately think of that will not work with ToB installed is The Darkest Day, and even then recent versions (1.3) do work.

The length and quality of mods varies, without knowing which ones you are installing its hard to say how well they will work. TDD is known to be buggy. Tactics is fairly stable. Depends on the mod in question.