Yes, you can use multiple Time Machine backup disks as long as you are running Mountain Lion OS X (10.8).
When you have two such backup disks, for instance, Time Machine alternates its backups between the two disks.
More details are explained here:
Time Machine as it exists in Mountain Lion is not capable of being set up to save just one User account to one backup hard drive and another User account to a different backup hard drive. As steve626 mentioned above, you Can set up ML's version of Time machine to back up the entire internal hard drive of your MacPro to two alternating external hard drives.