Windows Backup and Restore works for making an image and using it to image a new drive. From you question, it seems like the Windows folder is on the ATA drive, is that the case? But Windows Backup is limited in the size of replacement drives. Since it looks at all the partitioned space on a drive, you cannot use a new drive with less room than that amount of space.
What you need to remember is the primary drive set in the bios is very important, because that is where the boot files will go during an install. If you do not want any chance of having an install go where you do not expect, disconnect the other drive.