What's the model number of the two SCSI drives?
If they're two generations behind current generation (e.g. Cheetah 15K.5) then they'll be most likely be slower than your Caviar Black 1TB under the usage you've described.
Those are mostly big chunk files so they won't benefit from the high rotation that 15K SCSI drives provide which are more suited to database files (small random read/write).
If those SCSI drives aren't too old (less than 3yrs old) you could probably still sell them at good price. People who buy 2nd hand server for small business database loves those.
Partition is useful for separating OS+app from storage data. So nuking the OS to clean install won't affect the other partition(s).
If it's purely a data storage drive then I personally wouldn't bother with partitions.