I recently bought and installed a PCI Controller RAID Card Adapter so I could use my new SATA hard drive as a master on my IDE computer. Installation of the adapter went fine, but I'm not sure how to set it up so that the SATA hard drive that I've connected to it runs on its own as a master. How do I do this? The PCI Controller RAID Card Adapter looks similar to the one shown here: http://www.newegg.com/product/Produ...

The card has its own onboard bios which you can configure with the software that came with it. You may have to go into your own computers bios and turn off the boot from HDD so that it does not override the bios on your card.

Ok I have another question. Would I have to install windows onto the new hard drive with a CD? or can the drive successfully run as a master with just being a clone of another working hard drive (of let's say, this computer)?

You can make an image of the old drive and transfer it to the new sata drive, you will need to make it the the first boot device in bios. SATA drives are all master, there is no slave/master switch. When you have yourimage transfered to the sata drive, disconnect the old IDE drive so you know it's working properly. Once all is ok, reconnect the old drive if you want and make sure that you set the bios so that it's set after the sata drive in the drive options.