Typically you have to choose one type or the other. At least when I bought my last motherboard last year that was the case with mine. I had to select one or the other in the bios. If things have changed since then I do not know.
from what I have seen you can use SATA II drives on a SATA controller, just won’t be as fast as SATA II’s throughput.
also with windows install I have had to have the SATA driver floppy available during install for windows to see the drive before it will install to it.
In my experience you can you both. You have to define which will be the “primary” in the BIOS (whether it be IDE or the SATA). Whichever is primary will function as your boot drive.
SATA II drives are compatible with SATA connectors, but they will be slower.
Vista will PROBABLY install without any SATA driver disk, but it may need one. IF you use the BIOS to have your SATA drive emulate IDE rather than SATA RAID then you will probably not need a driver disk. If you’re trying to run SATA RAID then you probably WILL need a driver.