You don't need to use software to install a hdd. The software they send can be of assistance if the drives don't show up in Windows, but that is not your problem here.
To get both drives to show up in My Computer, go back to the Disk Manager and on right click on the new drive. Select Write Signature (or something like that). I think that opens a Wizard, just follow through it. I believe that will also take you through setting up the partition. If the drive still doesn't show up in My Computer, go back to Disk Manager and right click just to the right of where it shows Disk1 and select Create Partition (or something like that). That should open a wizard, just follow through it.