If you are moving the drive to a new computer it's always best to have a clean install, due to possible problems related to motherboard specific drivers etc. I'm not sure exactly what you're trying to do, but it's always best to install the OS to C drive, which will be on the Primary IDE channel, and therefore the new drive.
You can partition the new drive into multiple partitions, and therefore use one for the OS, one for games etc, and so on. I always prefer to keep partitions under 8GB. That keeps the OS and other programs, games in your case, on separate drives. It also allows a separate partition for backup purposes, or to save files that won't be lost if you have to format and reinstall later for some reason. The old drive can serve the same purpose.
As for the old drive, if you don't have anything you wish to save on it, such as documents, pictures, sound files, etc I would format it and install it empty. Don't use the /s switch, which copies system files to make it bootable. Use that switch only on C drive. If it has files you wish to save, install it then transfer anything you want to save to a partition on the new drive, then format it. I don't recommend trying to uninstall or delete Windows to clean up the drive. Formatting is best.
Any applications on the old drive you wish to use are best reinstalled fresh on the new drive, trying to copy them from the old one will most likely result in problems with missing registry entries and misdirected links. That's things like MS Office, Front Page, Scanner software, etc.
If you're trying to set things up so you can use the old drive, as slave, to run the OS, that's a whole new ball of wax, and generally not recommended, unless you're really good with computers...keep the OS on C drive.
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