I'm planning on using FreeNAS on a SUPERMICRO MBD-X9SCL-O motherboard that has built-in RAID controller , would the freenas built-in drivers for RAID work with this kind of motherboard ?
FreeNAS\FreeBSD doesn't support the on-board RAID controller, which is the same Intel RAID you see in their desktop boards. That said, you should take a look at ZFS and use that for your filesystem\volume manager.