You mean you have both the FillDB and the MSSQL DB on the same RAID array?
That is definitely not a good idea. A large/slower RAID 5 for bulk storage of the download cache is a good idea. Something like the Intel S3700 or similar PCI Express storage is best with frequent backups to an internal RAID array that then gets shipped off elsewhere is going to give you the best performance. Short of that, multiple RAID 1 volumes of SSDs for FIllDB, SQL, etc… are a good idea.
How many endpoints in this environment? How many console operators?
Also, see: FillDB Buffer Size Issue - #4 by jgstew