Can you run the Windows GPU client via wine with X running?
Yes, just install and configure everything needed to run the Windows console GPU2 or GPU3 client as you would for a headless system. Running X, open a terminal window and run your wine F@H command line in the directory where the F@H GPU executable is installed.
Also you install a second GPU in a system? The GPUs will not run in SLI mode since the MB does not support it.
Yes, you can run a second client on a second GPU card. You do not need SLI (actually I think you cannot use SLI.) As you would on a 2 GPU headless system, install and configure a second GPU client in a separate directory. Open a second terminal window and run the command line in this directory.
My setup is described here: http://foldingforum.org/viewtopic.php?f=54&t=14971
. I have since upgraded to wine-1.2-rc3 and moved the DLLs/symlinks to ~/.wine/drive_c/windows/system32 directory. Moving the DLLs was the key to getting Core 15 with the GPU3 client (thanks to Hyperlife for the solution http://foldingforum.org/viewtopic.php?f=54&t=14673&start=300#p152014