... what are AHCI drivers ?
They are advanced performance drivers for the SATA controller in your Mac Pro. When you go to profiler in OS X and bring up ATA you will see that your disks will all be connected by AHCI protocols.
Windows natively uses legacy drivers instead of AHCI when you install it on a Mac. It is much easier to select AHCI on a BIOS machine. On an EFI machine as the Mac, you have to tweak it with some nasty tricks to run the AHCI drivers. It is not a simple matter of just installing them. You actually have to edit your Master Boot Record inside the GUID or MBR partition table. I will come to that later.
With legacy drivers installed your RAID array prevents Windows from recognizing other SATA drives as internal. The array absorbs the addressing in those legacy drivers I suppose. You can remove the RAID and do everything you want. After installing Windows you can put the array back in and it will run. So one way of doing this is to clone OS X to a single disk and fit that disk. Then you do your Windows stuff. When you are finished with Windows you remove the single disk and refit your array.
Now to the AHCI drivers. You need to download Intel Matrix Storage Manager
http://downloadcenter.intel.com/Product_Filter.aspx?ProductID=2101 from this adress. You also need the floppy disk facility that you find there as well. You can also use an older version which nanofrog posted here
http://www.ShareCow.com/Download.aspx?request=b64424d0-2cd3-4c81-b46f-390b8e7ca359 When you have made those downloads put the folder with the floppy facility on a USB stick or burn it on CD. If you are hell bent to use XP you will actually need floppies because XP will not let you use other means. Generally XP isn't desirable on a Mac Pro because it is only supported in 32-Bit and not in 64-Bit which will render most of your RAM (above 2 GB) memory useless. The 64-bit varieties of Vista and Win7 have 32-bit emulations installed which will allow you to run any 32-bit program. So they are much better to use. A word of warning to 2006 and 2007 Mac Pro owners. Your machines use a 32-bit EFI. It will not be able to read Windows install DVDs with multiple images like the anytime upgrade DVDs. The 32-bit EFI boot loader freezes when you try to load an install disk with multiple images. The only known workaround at this time is reducing those disk to single image with the vLite program.
When you are installing Windows you should load the AHCI drivers from the floppy facility (actually from your USB stick). In Vista and Win7 you do this from the installation window where you can format or partition drives. In XP you have to hit the F6 key in the beginning when XP starts to load from the optical disk. When you have installed Windows load your drivers from the hybrid Leopard disk. All Leopard disks have a Bootcamp driver image on them which is acessible under Windows only. For 64-bit Windows you need to execute Bootcamp64.msi with admin rights. You find it in the drivers/apple folder on the leopard disk. If it is not there you have a very old version and need to source those drivers somewhere from the internet. There are torrents and downloads from rapidshare. Google Bootcamp 2.0.1 for that. In Win7 you have to apply compatibility patch to Vista drivers before you can load the program. Right click the file and select the routine for compatibility.
When you are done and have installed all the updates you need to activate the AHCI drivers. They will not be running at that stage. Copy the instructions from Ludachris at
http://www.insanelymac.com/forum/index.php?s=&showtopic=126089&view=findpost&p=939694 . Download the patch from Johnsock. The next step is editing the registry as directed by Ludachris. Next go to disk utility in OS X and make a list of the identifiers of your installed partitions. There is an info button which tells you the internal name of each partition. Make a paper record of the partiton name and that code. You will need this later when you have no access to disk utility. Finally here make a backup with Winclone or at least set a restore point for Windows to get back to that stage if you screw up the next step.
The next step is executing Johnsocks patch program. Pay particular attention to patch the right partition/disk. For this you will need the codes that you have noted. The program tries to find your Windows disk but you have to make sure it finds the right one. It often suggests a wrong disk. When you are done with patching your MBR you shut down Windows and restart it. Then you bring up the Windows device manager. Go to ATA devices and click properties and update drivers. Disregard all automatic searching and force the system to load the AHCI driver from your USB stick, CD or floppy. For non Nehalem Mac Pros the right controller is ESB2 for Nehalem I believe it is ICH10. If the system tells you the driver is wrong disregard that and force the driver to load. Then shut down Windows and restart. If you have done the patch right and selected the right controller for your chipset Windows should now use basic AHCI drivers. If you got it wrong windows will malfunction on load. You can use special load options to go back to the last known good configuration which you hopefully established by setting the restore point in the last paragraph or you can restore Windows by Winclone. Start all over with this paragraph until you got it right.
We are now ready for installing the Intel matrix storage manager. Run your downloaded executable file and restart Windows. In Vista and Win7 you have to run it as administrator. Now you should be all set.