I have an ultra d, and AFAIK you can only control 3 fans from the bios - 2 of those are the cpu and chipset fans. So that leaves only 1 fan left, and it's the one near the cpu fan connector. You can set the fan to turn on only at a specific temp and to go full speed at a specific temp using the bios. I think it's in the PC health status screen.
Also, I have 2 case fans connected to the board, without any instability issues, and this is in a rig where pretty much everything is OC'd, and using the 5v line on the mem.