I'll take a shot at answering this, but it's a huge wide open question.
You have three possible setups here: Lone 500, two separate 250s, or a RAID 250 (set up for performance not redundancy.)
The advantage of the single 500 is all your stuff is in one happy place and you have all your bays open for expansion in the future.
If you take the two 250s, and put the OS on one drive and all your media on the second (all your music, photos, etc.) you'll find your system is a little snappier. Especially in machine like the Mac Pro, your bottleneck is going to be the hard drive. By allowing the machine to use both drives during normal operations, your speeding up those operations.
The other option is a RAID set up. If you don't know about RAID, your best bet is to go look it up. Depending on how you use your computer, that may get you the advantages of a single drive and reading/writing to two drives, although it does double your exposure to hard drive failure.
good luck.