Backing up drives on Mac Pro

I'm wondering if it would be possible to back up each internal drive with time machine separately. i.e. internal drive bay 1 backup to one external, bay 2 to another external, etc.

No, sorry. Time Machine can only have one set of instructions (what to back up and where) at a time.
It can back up from multiple volumes, but only to a single one.
A better option might be to use Time Machine to back up your OSX drive to one external, and use a different app to back up other volume(s) separately.
[CarbonCopyCloner|http://www.bombich.com> is donationware; [SuperDuper|http://www.shirt-pocket.com/SuperDuper/SuperDuperDescription.html] has a free version, but you need the paid one (about $30) to do updates instead of full replacements, or scheduling.
And/or, see Kappy's post on Basic Backup.

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