Managing Hard Drives

I’ve got three, total: an OS/programs HD that’s partitioned between OS and programs so that if I have to nuke Windows, the games live on. There’s also a media HD stuffed with music, movies, and my writing/comics/photography. Finally, there’s my backup HD that keeps copies of the least-replaceable parts of the media HD (my writing and photography + the music and some of the older video stuff).

The backup HD used to be the media, as far as I remember. Nonetheless, when I look at it in disk management, it’s listed as active, primary, and system, of all things. I suspect that either the “active” or the “system” tag are the root of my problems.

The newest version of Ubuntu just hit, and I wanted to set aside ~50GB of my backup HD to Ubuntu, with the rest serving as backup (it’s high time for me to update the backup, anyway, so I was going to be overwriting it). However, Disk Management won’t let me format the partition on the backup HD.

If it helps, the backup HD is listed as Disk 0 in Disk Management, while my OS HD is listed as Disk 1. Is this a SATA wiring issue?

The OS HD is listed as boot, active, crash dump, and primary partition, if that helps.

Am I safe to format the backup HD and repartition it? Why won’t Disk Management let me?

And while I’m at it, what’s a good automated backup maker that will toss updated and new files onto the backup HD every 2 weeks or so at like, 3 in the morning?

Edit: According to wiki, the system partition stores the boot loader, oddly enough (not the boot partition?). I assume that nuking that would be terri-bad. . . so how do I transfer that easily?