I don't think it'd be a problem. I've not used serial ATA, but I'd assume it'd work as an additional controller, and not exclusively. I've got a RAID controller on an Epox 8RDA+ motherboard - 2 HD's attached to the RAID controller, and one on the motherboard's regular IDE controller. The RAID array is drive C: and the motherboard's hard drive is the F: - there's also a ZIP drive and DVD drive on the motherboard's IDE controller.
If you are going to set up Windows, make very sure that it is installing on the RAID array (assuming that's what you want), because Windows will most likely see the regular IDE drive FIRST, and assume you want to install Windows to that drive instead.