I would suggest not using the motherboard RAID setup. I use all linux software raid on my servers. It works very well, and is safer because you arn't dependent on a specific motherboard or controller card.

The way I setup my system is this:
1GB mirror raid for root filesystem
(optional) 10-20GB mirror raid for OS filesystems (usr/var/tmp/)
Raid5 for the rest of the disk for /home

software raid is great because you can divide up disks into several raid sets, instead of having to do one type of raid for the whole disk.