What you want can only be achieved by removing the two disks, installing the new one on its own, installing Windows on it, installing all the software you need on it.
After that, add the old disks back into the system and move over any data you want to keep (or better yet, burn all that data to CD or move it to a network location before you remove them so you don't have to move them back).
SATA doesn't have anything like masters and slaves, that's all handled for you. Just plug the disk on a SATA cable, add a SATA power cable, and turn on the machine.