Most bios setup programs on SLI or Crossfire boards have an option that allows you to choose which PCIE slot to look at first for the video card. That way, the decision to use either slot can help if you've got a cramped, smaller case.
Trying to fit one or two of the newer, longer dual-slot video cards into a mid-tower case can be quite a chore. When I built my new unit with a quad core X3360 and twin 8800GTX OC's into an Antec P-180 case with three hard drives and twin DVD burners and a 1000 watt PSU proved to be just too much work. I went out and bought a Thermaltake V8003WBS full tower case and it made the build much easier.
(Hoisting that steel case around and getting it set up on top of my desk did wonders for the biceps!)
I loved the Antec case. It was quiet and would fit anywhere, but it was just too small inside, especially with the PSU mounted down in the bottom of the case. Trying to do a neat job of wiring would have been a nightmare.