It's always fun when you stumble on a solution to a problem, but even more fun when you stumble on a solution to two problems. I have an external hard drive that has two partitions that mirrors my main hard drive every other day (so I have two backups staggered by a day), and that's working nifty for me. The problem is that they've been stuck on my desktop, which takes up desktop space (not that I have a packed desktop anyway... it's the principle of it- I like clean). My other, more real problem, is that in certain areas OS X scans hard drives for apps. IE, when I have a file on my desktop and I want to open it with another app, I right click -> open with, and then select the app. The problem is that OS X scans for other apps on my drives, so it spins up my external hard drive which takes 3-4 seconds of my time.
I was randomly googling around and found that if you unmount your drive or partitions in Disk Utility, it'll remove them from your desktop and will solve the scan-and-spin delay I had, too. The additional bonus is that it appears that disk backup software can smartly handle this- Synk, my preferred backup solution crafted by a couple of fellow Carnegie Mellon students, is among those apps that can do it (SuperDuper can apparently handle this just fine too). Synk is scheduled to do my backups in the wee hours of the morning, so it now automagically mounts the correct partition, backs up to it, and unmounts it so I'm ready to go when I wake up in the morning.
I love technology.