doesnt matter.
i find that if i plug my 7800gt into two monitors, both display the same thing. same thing goes with using both dvi's and the s-video port (plugged into a tv) too. i mean, i dont know for the 6800gt but it should be identical video.
btw "performance" settings just means "low" settings, thats why it gave you higher fps.
cs has much worse graphics than most games, which is probably what makes it such a good multiplayer game. almost no-ones computer lags during the game. if you still think it doesnt look as good as it should, then just max out all the settings at highest quality and see if that helps. personally, id prefer higher quality picture with 60fps than lower quality picture at 100fps. slower easier gameplay, higher quality picture, and most games limit fps to 60-75fps anyways...
i mean there are exceptions i knew a guy with a pentium 3 and some 64mb graphics card with i think 384mb of system memory and a 10gb hard drive.. dont ask me how he got it to lag, but it did on cs 1.6's lowest settings... it was horrible...
it seemed like his system shouldve played the game though... he probably just had his memory backed up too much with other programs like an anti-virus or something...