Another thing that's occurred to me which should help, if you are going to use SATA drives makes sure you set the BIOS to use AHCI or it'll treat them like IDE drives (ie you can't use NCQ). If you do use AHCI then make sure to download the correct drivers to input when you install windows (ie you'll need to hammer F6 as windows begins to install (it does prompt you but not for long)).
If you want to use RAID (oh and raid 0 is the fast one, raid 5 would be a bit of a waste of time for a games machine) then you'll need to do the same except setting the BIOS to RAID and getting RAID drivers on the floppies.
As an aside, consider getting a hard drive just for the things you wish to keep. Then should you need to reformat your computer then all those downloaded drivers, saved games, emails and whatever can be kept nice and safe on that separate hard drive.