The problem is that Vista found the boot sector on the WD 500GB and thus just used that for your second install. Of course, this isn't what you wanted. What you should have done was unplugged the WD 500GB and then installed Vista on the RAID0.
However you could of avoided this whole mess from the start and just installed Vista right onto the RAID0. The Vista installer gives you an option to select and partition your hard drive.
You might be able to fix this using the Repair option of the Vista installer (boot from the DVD and you should see it), but I haven't really used it.
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