There is an internal flash on the DR. You can't access this directly (that we know of), except through scripts. Take a look at my updated CTB script. This is a modification to an internal iRex application. I copy the updated binary from the SD card to the internal file system.
You can modify any of the programs found here:
http://developer.irexnet.com/pub/iOn/Sources/1.0/
As far as I can tell, the bottom connector is for a serial connection. I don't know much more than that (or if that's even accurate). iRex hasn't release any plans or specifications.