Pineapple is right - the external bays are aligned with openings in the front of the case for devices such as CD/DVD drives, card readers, or floppy drives that you need to be able to insert media into. The bay is INSIDE the case, it's just that it's front end is accessible from the front of the case.
The internal bays have no corresponding opening in the front of the case, so you couldn't put something like a CD/DVD drive into them. They're only for hard drives that require no user access.
As sub mesa suggested, you'd use eSATA with a drive in a separate external enclosure, not with one of the drives in the internal or external bays in your case.