I have a pcie Matrox G550 catd I have the Kernel source and I am tring to find out what to change so my Matrox catd will work under pcie

Can you explain in more detail what you're trying to do please? PCI an PCI Express are, as far as I know, different "form factors", so a PCI card won't fit in a PCIe slot and vice versa. If you've not done any (kernel) programming before, then presumably modifying the kernel is going to be quite a difficult task. Of course, this assumes that you actually need to do that, which may or may not be the case, depending on the exact nature of your problem.

PCI and PCIe are not only different form-factors, but also technically complete different. It is simply not possible to run a PCI card in a PCIe slot or vice versa.

Does the card show up at all in the system? What does lspci -v show?

I have the pcei profile I just need the driver for pcei

Well, the driver for Matrox cards that is included with X.org is "mga". See "man mga" for more information about it. The man page suggests that it's only for PCI and AGP cards, but I visited the Matrox website and downloaded their tarball for your PCIe device and the man page is identical. You might not have the package installed, but it appears from your profile that you're running Fedora, so someone else will have to help you with that.

Also, this has nothing to do with the kernel, so I've reported it for moving to a more correct forum.

Then your thread-title "matrox G550 pci vs pcie" is very misleading, you should correct that. In general, support from Matrox for Linux (sadly) is very bad. I would rather think to get a different card instead of putting any effort into that.