I'm just about to quit using my nVidia boards built-in RAID
RAID cards vary a lot in price. Just be aware of the difference between the "software" RAID cards and the "hardware" ones; i.e. where the XOR calculations are done.
You could always leave your single disks connected to the motherboard - in fact might be better that way so long as you don't need to transfer data between the RAID5 and the single disks.
If I may ask, why?
If you're watching videos, then a software-based RAID5 setup is probably not going to be that bad. However if you're running databases, encoding HD video, etc. then you want to stay very, very far away from it.
The problem you have is, if you RAID the drives in Windows then you'll have to break the array when you get a proper RAID card. Will you have a way to back everything up?