Thats a good question.

You need to keep 2 physical machines to attach the fpga boards too. However I assume you are correct in saying that it doesn't make sense to keep the graphics cards in there. Weirdly FPGA.contract do have GPUS on the go (
http://contract.fpgamining.com/?page_id=34).
Oh, and in another rectification, accordding to the wiki (
https://en.bitcoin.it/wiki/Mining_hardware_comparison) a real life quad 5850 machines pulls 700 wats but only generates about 1360 MHashes.