I'm currently running Vista 32-bit on a fakeRAID 1 array. I was going to put Linux on the array to do C development but I have some old hard drives lying around so I'd like to use those instead. My question is, if I drop a third hard drive into my computer and install Linux on it, what will happen when I try to boot? Will the Windows boot loader recognize Linux? Will the Linux boot loader manage the booting of Windows and Linux?
First, be sure that the third harddisk is numbered last by BIOS. Otherwise, you might not get Windows booting, and it might mess up for the second harddisk.
Then, after installing Linux on the third harddisk (which should be OK), the Windows boot loader will not know anything about how to bootstrap Linux.
The usual way to deal with this, is to let Linux manage the boot process, by installing grub on the first harddisk. grub is able to boot Windows as well as Linux and other systems, letting you choose at startup. If you install Ubuntu, it will install grub and also autodetect the Windows installation.
Finally, remember to take proper backup of your two Windows harddisks before doing this!