The only time I've had a SATA drive listed as an IDE device is when lightening struck at my neighbors and permanatly damaged the drive. Your SATA II drive should be seen in your BIOS. Here is the information from device manager and dxdiag (system devices). My system has two onboard controllers along with a PCI RAID controller. At that point, your SATA drives should be seen and operational.
After the OS is installed and the onboard SATA controllers enabled, the drivers are installed and system rebooted. This is how I do it, but it is a matter of preference, not correctness.
#Silicon image sil3132 softraid 5 controller non raid install
On my mobo, IDE compatibility mode (selected in the BIOS) allows you to install an OS on a SATA drive without selecting F6 and using driver diskettes. I know you've done many builds, so if this reply is too simplistic, its meant with good intentions.