I've got a Windows 7 installation image on my USB hard drive, which is set up to be bootable. I know it works because I've used it on several computers, and it works on the computer I'm trying to install as long as the RAID controller is disabled. However, when I enable the RAID controller and attempt to boot from the USB driver, it hangs for 30-60 seconds and then gives me the "disk boot failure, insert system disk" error like it can't find any OS. Just for laughs, I disabled the RAID controller again and it booted fine. I'm having separate, unrelated issues burning a dvd with the ISO, so I would prefer to get this working.
Your Windows installation needed to have the AHCI raid drivers for the motherboard "slipped in" during Win installation. When you first start installing Windows, you will see a notice to press F6 to install 3rd party controller / raid drivers.
In your current installation on the external drive, Windows doesn't recognize the motherboard's raid controller and therefore won't boot. This is true for any raid boot setup. Microsoft has, however, has included the most common older raid chipset drivers by default with every version since XP (pro) and up, though these are usually dated and for enterprise level raid array cards that most consumers don't have access to or need.
You MIGHT, however, be able to install the mainboard's sata driver AND sata raid driver from another computer in your external setup - I'm not sure as I've not tried to do this after the fact in my installations and I've never run anything but *nix from a portable device or CD.
Your motherboard manufacturer's website may have information about raid setup. This is a fairly common question in today's gaming influenced performance trends and often discussed on the manufacturers' websites.