[Halcyon]

You may need to load some SATA drivers when installing Windows. These will have come with your motherboard CD.
You dont always have to use the extra drivers, it depends on the setup.
If needed, you will need to press F6 (If I recall correctly) when it reboots to install these drivers.

It is very much possible to have the Hard drives configured the way you say and there should be no problem with this configuration.

If you need drivers, check out your motherboard website and it should have them on there.