Are you sure you have two hard-drives or one hard-drive that was partitioned into 2 drive letters? You can move your data to the second drive, and you need to do it manually. I would not start installing programs into the second drive.
The simplest way would be to move the contents of My Documents to the other drive (or patition, whatever you have). Right-click on My Documents > Properties, and change the location to the other drive letter.