This is for Windows XP (and prolly 2000 also)
If you want Windows to be by itself on it own partition without anything else, you can completely redirect the location of your Program Files folder and your My Documents/Music/Pictures folder
To redirect your My Documents/Music/Pictures folders, just right-click it on your start menu and change the location from the "Target" tab
To redirect your Program Files folder:
Go to Start>Run type in "regedit"
Navigate through to HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion
on the right window you should see ProgramFilesDir
just double click it and change the drive letter to whatever partition you want your programs to default to installation to.
Also, Raptors are too expensive, it would be cheaper to just get a similar size RAID array and then you would actually get even better performance too.