If you have the empeg plugged into the dock, and are powering it off of the AC adapter, it may be in AC mode and not think you have a tuner attached. I'm not sure what needs to be done to allow a tuner to work when powered off of AC (check the threads involving Mark's Docking station), but using setting Hijack's Force AC/DC mode to DC might do the trick. It will still use AC, but run as if it's in the car.

The phono jack is to hookup a Sony Stalk remote control. The pin-outs are documented in the FAQ.

The dial allows you to specify the radio, and is related to Mark's Docking station (it's been a while, but I seem to recall that specifying a specific Tuner ID would let Hijack know it was in one of his docking stations.)