I’d evaluate how I’m gonna set up my data first.
If you use Windows 2000 or XP, you can setup partitions from within the OS itself.
Backups should be done to something other than a hard drive. I have mine go to my file server and I back them up on CD-RW. That way, in the event that all my machines are shot (It’s almost happened once----damn IBM!). If the hard drive craps out, it won’t matter what partition it’s on—please understand that. Some games that can be copied and run from the hard drive I will do that with them. Everything will have to be reinstalled, but any files that are on a different partition will still be there. It’s not as good as a complete mirror of the hard drive, but it does save you having to recopy alot of data over.
On my main box, the average size of the partitions is 5GB. Sizes range from 1.5GB to 13GB between my two drives. Some of the games that take a while to load (namely Unreal Tournament) are on a game partition on my 7200RPM hard drive. I have most of the stuff I’ve downloaded go strait to a partiton on my 5400RPM hard drive since it’s got a total of 40GB.
I use partitions as something of a grouping. Keep similar things together so that you have less work to do when you have to reinstall Windows.
If you are running Windows 95/98/ME, I do believe there is a limitation on how large the disks can be, so you’d need to have at least 2 or 3 partitions (no larger that 40GB). I’m not sure what OS you’re using, but there are some differences between Win9x and WinNT (NT/2k/XP).
For the extra drives you have, I’d just have 'em as spares. However, if you want to hook them up, I personally like having each IDE drive on it’s own channel, since IDE devices can only be accessed one at a time.
Don’t rely on a hard drive for backup. These are mechanical devices, which have moving parts that will break down eventually, some sooner than others cough IBM cough. If you want to back up, do yourself a favor and buy a CD burner. Doesn’t have to be blazing fast (although that’s not a bad thing), but don’t depend on a hard drive—you will get burned.
edit: Dang, Syngod beat me to the punch.