Just today I've been tinkering with a two GPU system for the first time. I guess it could have been bad luck/timing, but I was trying to get both GPUs running on BTCguild with phoenix on high aggression and had a lot of network troubles/idling workers. Once I switched one GPU to slush's and the other to BTCguild (also worked when I tested Eligius) all of the network/idling problems went away. Also I suspect I have worse latency to the US than a lot of people.
So basically - this is completely anecdotal advice and I really don't know how the system is "supposed" to work, but after a couple hours of testing my conclusion was: mine in two different pools for best results