I do not have a 3rd party RAID card installed in my Mac Pro, however, I can confirm that you can definitely install CentoOS 5.2 x86_64 (64-bit) on the Mac Pro (2 x 2.8GHz QuadCore) from http://mirror.centos.org/centos-5/5.2/os/x86_64/
I currently have Mac OSX 10.5.6, Windows Vista Ultimate 64-bit and CentOS 5.2 64-bit running happily all on their own seperarte HDD's. I can choose which one to boot from by holding the "Alt" key down during power-on.
I did a network install from the CD ISO image.
So nothing got ruined by the linux install, I removed all the HDD drives from the Mac Pro and just put a spare HDD in the 4th HDD bay, which is dedicated to CentOS, once your installation is complete, you can just push-home the HDD bays you removed. You can then choose which OS you want to boot from by holding the "Alt" key down during power-on. The CentOS installation will show as a hard drive icon, with the text "Windows" underneath it!
The important thing to remember, is to hold down the C key to boot from the CD. Secondly, and most importantly, the screen will stay grey for a time while the CD boots the vmlinux image, etc. Be patient, eventually you will see the CentOS installation process.
From here, you just install as normal.
In terms of support for the nVidia 8800GT card, you will need to download the drivers from the nVidia website, after you have finalised the installation of CentOS. However, in order to install these drivers, you MUST install kernel-devel RPM using yum, without this, it will not install. The nVidia installer does guide you on what dependencies it requires, but follow them very carefully and you will succeed.
yum install kernel_devel
You must change to runlevel 3 in order to install the nVidia drivers. I think you can just type: init 3 from shell. However, I took the nVidia advice and edited my /etc/inittab file and change the runlevel from 5 to 3, rebooted, installed the drivers. Once the drivers were installed, just edit the /etc/inittab file and change back to runlevel 5, reboot. Job done!
Another extremely important thing to mention, DO NOT install any updates until you have turned-off SELinux and have rebooted. If you don't, the updates will get installed incorrectly, because of permission problems, and when you reboot your install will be permanently broken. I couldn't work out how to fix it, so I learnt that the hard way!
If you need any help, please feel free to post back here, I'll receive post notifications.
Best of luck.