No it won't. However, you won't be able to really use the desktop while gaming. Mainly have chat clients/email open, and you still have to alt+tab out of the game.
OP, also, I've been running trip screens for a bit now
A little googling and I think I can get the few games I have to play in windowed mode, at full single monitor resolution, snapped to any monitor available. I was reading a little about that. With this config, you only have to Ctl+ALT to desktop, but when you click on the second monitor it wont go back into your game. I had that problem before, until I did a bit of reading. I only had dual monitors set up for a little bit(couple days), on a 9800GTX. I didn't try any gaming during that time to check performance. I was using the setup for audio and video editing.
Edited by PDXMark - 9/25/10 at 2:24pm