As Barfish mentioned, the compatibility issues do not come in with the selection of GFX card and CPU, but rather when you select Mobo/CPU.
It is highly unlikely that PCI-e cards would not work on a mobo that supports PCI-e (given that you install the most up-to-date drivers). The Mobo/CPU combo on the other hand is not as straight forward as that. I bought a new system a few months ago and went for a XFX mobo with a 680i chipset, I thought of going with the E8500 cpu, but at that time, the firmware of the mobo did not yet support the Wolfdale series of cpu's. I had to go for the Q6600 instead (which I love dearly).
If you are not to comfortable with our non-professional solution to the problem, maybe you can try to google it and see if there are any other peeps out there with a similar problem.