Ihmo, qwerty8990's 12-June-09 thread at http://forum-en.msi.com/index.php?topic=127761.0, is a good synopsis of how to initially setup RAID 5 for performance.
Four years later, I have a related question that I haven't seem to find a definitive answer to. My question stems from the fact that I recently encountered an "old man" 5 disk RAID 5 array that has issues. It's striped ok (ie. 64KB stripes), but there are two other problems.
1) The Cluster size is only 4KB, where 64KB would be better for the MSSQL data mdb's that this host drive is used for, and
2) The single NTFS partition on this host drive is not aligned.
The hardware is an Intel SRCZCR Raid Controller, with a 10 SCSI disk hot swap backplane populated as follows: Win2k3 Server OS on RAID1, MSSQL ldf logs on RAID1, and MSSQL mdf data on 4 disk RAID5 (ie. 3data+1parity), and 2 pooled hot spares for good luck.
( Fyi, the server itself is an "old man" 2003 Intel SC5200 Server with Intel® Server Board SE7501HG2, with the optional Intel SRCZCR Raid Controller, optional 10bay Hot Swap back plane with 10ea ST336607LC 36-GB 10K U320 80-Pin HDDs , and optional 3 Hot Swap power supplies. 2ea Xeon 3.2GHz CPUs, 4GB registered ram. )
If I'm not incorrect, something like Acronis Disk Director can take care increasing the Cluster/AllocationUnit size on an existing data partition (RAID or non-RAID), however I'm not sure about using today's 2013 vintage alignment tools on a RAID5 array with existing data. If anyone has any experience on this kind of surgery on existing array drives, I'd certainly appreciate your comments and hearing about your experiences.