Off – disables the embedded controller. Should be pretty obvious what happens here.
ATA – sets the controller to ATA mode. Basically, sets the controller to act like a regular ATA controller.
QDMA – Queued DMA: sets the controller to support higher transfer rates than PIO. A driver must be installed to use QDMA mode. Using this mode, you’ll likely need to inject a driver during your install sequence to recognize any devices connected to the controller.
RAID – sets the controller to RAID mode. Would allow you to setup RAID levels across multiple devices connected to the controller.
Just to clarify if it isn’t already clear: These settings will impact the embedded ATA controller (if you have a CD/DVD drive, it’s likely connected to the ATA controller). It would not have any impact to the PERC Controller.
So, lets move on and tackle your actual problem: What kind of disk performance are you seeing and what kind of disk performance are you expecting to see? Is it slow on reads/writes/both? What kind of performance testing have you done to confirm the performance? What kind of (and how many) drives are attached? How are the RAID1/10 arrays configured (ie: 2 drives, 4 drives, 8 drives in a RAID10? Is there a battery backed write cache and are you using it?