I have four HDs in my 2008 MacPro. One of those is dedicated to TimeMachine to backup the other 3 drives and my wife's Mac Mini. So, TM can certainly backup multiple drives.
That being said, TM is not a great choice as your only backup system (particularly if the TM drive is stored locally). It's great for onsite backup, so you can retrieve something that you deleted, or restore a corrupted file. However, for catastrophic issues, you should make sure you've got a more robust backup system in place.
In addition to TM, I also use Carbon Copy Cloner and an external 2 TB drive. I have the disc divided into 4 partitions, one for the Mac Mini and three for the drives in my MacPro (I don't bother backing up the TM drive). I store the drive in my desk at work and bring it home once a month to perform backups. This way, worst case, I would never lose more than a month's worth of files. Not the perfect system, but a heck of a lot better than relying on TM only.