I have an SSD I want to run in AHCI and a large standard hardrive to run in IDE. Can I run both in different modes on the same machine or does AHCI mode apply to all drives?
Why would you want to do that? Your regular hard drive will work fine with AHCI mode. One thing you need to factor in is... extra drivers would have to be loaded on boot and could add a few seconds to your boot time into Windows.