Are you saying two different drives in one box? One has to be set to slave and
the other master. Please check the jumpers on the HD to insure that one is slave
and one is master. Most like the boot grub would be on the master drive. I did
have to use gparted to mount my second HD. I Upgraded from a 40 gig to 180 gig
and transfered all my data to the second drive

The secondary drive is set at slave, but it fails - either with an error
message about the drive not supporting cache, or when trying to
initialize the USB drivers. I've been told that it was set up on
hardware similar to my own (this isn't my drive, working on it to show
someone how to set up a Linux install), and that it has run before.

I have Ubuntu booting off the internal hard drive and Fedora 7 on an
external USB (on a laptop). If you're talking about installing another
Linux distro on a USB drive (or stick) it's a little more involved as
you have to rebuild the boot image to include the appropriate drivers
otherwise it won't recognize the hardware.

To install Ubuntu on an external drive (and hundreds or other Ubuntu
tips and tricks) I can highly recommend Ubuntu Hacks as an excellent
resource (published by O-Reilly and available on Amazon).

If you want to put Fedora on an external drive I can detail how I did
here if anyone is interested.