Just sharing my experience here 
I was originally running a 2008 2.8/8 with an 8800GT GPU, and wanted to up the GPU for Windows to something rather beefier - so I bought a BFG GTX 275. I was expecting some issues with running the cards, but it has been perfect. My solution is:
OS X:
1) Power lead to the 8800GT in Slot 2, no power to the GTX 275.
2) 30" and 23" plugged into 8800GT, both working
3) OS X boots perfectly, doesn't see the GTX 275, and hence the fans don't go into overdrive
Vista:
1) Power leads (two 6-pin off mainboard) to the GTX 275 in Slot 1, no power to the 8800GT.
2) 30" Cinema Display plugged into GTX 275, works fine
3) Boots perfectly, works a charm. Vista doesn't see the 8800GT and hence doesn't get into a tizzy over which card to use.
Notes:
Mac Pro is set to boot Vista by default, as I don't see any image on screen until the Vista loading screens (ie: I can't hold down alt and use the Boot Camp drive selection).
Now, unplugging power/monitor leads is a little bit of a pain, but only takes around 30 seconds. I haven't had to go and bodge power from the optical bays (as I have two SuperDrives for a start) or an external source. The Mac seems to recognise the 8800GT in Slot 2 even when it isn't powered, enough for it to read the EFI ROM and allow booting. Personally, I find this a far easier, and tidier, solution than the ones presented so far (ie: with both cards running).
I was originally running a 2008 2.8/8 with an 8800GT GPU, and wanted to up the GPU for Windows to something rather beefier - so I bought a BFG GTX 275. I was expecting some issues with running the cards, but it has been perfect. My solution is:
OS X:
1) Power lead to the 8800GT in Slot 2, no power to the GTX 275.
2) 30" and 23" plugged into 8800GT, both working
3) OS X boots perfectly, doesn't see the GTX 275, and hence the fans don't go into overdrive
Vista:
1) Power leads (two 6-pin off mainboard) to the GTX 275 in Slot 1, no power to the 8800GT.
2) 30" Cinema Display plugged into GTX 275, works fine
3) Boots perfectly, works a charm. Vista doesn't see the 8800GT and hence doesn't get into a tizzy over which card to use.
Notes:
Mac Pro is set to boot Vista by default, as I don't see any image on screen until the Vista loading screens (ie: I can't hold down alt and use the Boot Camp drive selection).
Now, unplugging power/monitor leads is a little bit of a pain, but only takes around 30 seconds. I haven't had to go and bodge power from the optical bays (as I have two SuperDrives for a start) or an external source. The Mac seems to recognise the 8800GT in Slot 2 even when it isn't powered, enough for it to read the EFI ROM and allow booting. Personally, I find this a far easier, and tidier, solution than the ones presented so far (ie: with both cards running).
