As you can see on Supermicro-web, disk-ports on some of C606-based motherboards work, but only for sata and without raid. You can use those ports for stand-alone disks, but I would not do it. Maybe only for hypervisor itself, or pass-through. As it was said here many times, ESXi does not do disk-caching and relies fully on controller. This chipset-controller does not have any cache, that means poor disk performance (and when I say "poor" I mean "very-very poor")...
That's disappointing. What if I create a chipset-raid (software) and passthrough the raid to a particular VM, basically separating it from the main raid (hardware raid). I tried passing through a highpoint 2320 (firmware raid) card and it doesn't work.
If you create software-raid in bios, ESXi will still see it as 2 independent disks because it does not support/recognise software raid. Then you can pass-through these 2 disks to VM, and VM will see it as 2 disks too. You can not pass-through the whole motherboard, so VM will not see its features (i.e. bios-created software raid). Sorry to dissapoint you, but that's the way it is...