I'm not quite sure what you're trying to do here. If you want Windows on HDD1 and everything else on HDD2 for example then that's not RAID, it's just two disks running independently.
If you want to go with RAID then the level you choose is determined by your requirements:
RAID0 - maximum read/write speed but no fault tolerance, if one disk goes all the data is lost
RAID1 - mirroring, redundancy at the cost of capacity with the same data on both disks. No improvement in read speed and usually a write speed hit
RAID3 - basic parity based redundancy. All the parity data is on one drive so speeds aren't as good as RAID5 but a better value option than RAID1 if large capacities are required
RAID5 - This is the most common server RAID level. Data is striped across multiple disks along with parity data so that the array can still operate if one disk fails. With the proper hardware read and write speeds can be very high.
There are other RAID levels (6,10,15,50 etc) but they're not that common.
Basic RAID0,1 and sometimes 5 support is provided by motherboard SATA controllers but to do 3,5,6 etc properly you need an add-in controller card with some form of dedicated parity engine to get decent write speeds. Most cards also give you more than the 4 ports a mobo solution gives you.
