This applies to the 3u MDS, a SuperMicro SuperServer 6036ST-6LR, SC937ETS-R1200NDBP, uses the X8DTS-F mother boards.
This is a two CPU FRU in one 3u enclosure sharing a common disk backplane. Each CPU FRU have a mirrored pair disks as system boot drive, typically it they are drives 0/1 pair and 14/15 pair.
The LSI SAS2008 is the built-in SAS controller used for booting, to manage the RAIDs use the LSI BIOS. During boot wait for the LSI splash and press Control C to get into the LSI BIOS, note other devices (QLogic HBA I think) also uses Control C, so do it only after the LSI splash. There is MegaRAID GUI, but I was not able to figure out how to create a new RAID with it, a bunch of stuff are greyed out, so had to resort to BIOS.
Create a new RAID -
If for some reason you need to add more RAIDs, the BIOS might not give you the menu option, the RAID Properties selection SHOULD give a screen having various create RAID options, but if there are existing RAIDs already, it might not give this option. (version is v7.03.00.00 2009.10.12) I had to temporarily remove (with the power off to the system) the existing disks from their slots and only leaving the new disks I wanted to RAID, this then allow the create RAID window to show after selecting RAID Properties. After creating the new RAID, reinstall the previously removed disks (with power off to the system).
Activating the RAID -
For a FRU to boot from or have access to a particular RAID set, the RAID set must be 'Activated' in the LSI controller of that FRU, goto RAID Properties, and check the Drive Status, if it is 'Inactive' then this RAID will not be presented to the system, therefor can not be selected as a boot device or OS usage. You can also use SAS Topology to check the RAID set status.
To activate this RAID set, select Manage Volume then Activate Volume. For RAID 1 configuration, the Drive Status of 'activated' will show as Primary / Secondary for each disk.
If the FRU was replaced in the MDS, the new FRU will see the existing boot drive as inactive, you need to activate it and then select it in the system BIOS in order to boot from it. Make sure you select the correct RAID pair, do not mistakenly select the other FRU's.
Drive slot numbering:
The physical drive slot numbering order is from right to left (the label on the drive caddy could be different):
Slot numbering, front view. The labels on the drive caddies might not be the same.
[left side] 15, 14, 13, 12, 11, 10, ... 3, 2, 1, 0 [right side]