I assume you know about Wubi as an alternative way to run Ubuntu.

Two, or more hard drives will work just fine with Ubuntu as long as the
Linux is installed after the Windows. You shouldn't have to change the boot
drive in the BIOS as the Grub startup menu should find and include all
operating systems on all drives, as long as it is on the boot drive. That
is what I have: Win7, which came with my HP system on the first drive,,
sda, a drive for storage and sharing formatted with fat32, sdb, and Kubuntu
on a third Hard Drive, sdc. Any operating system can be chosen from the
grub start menu.