Transfers between empeg and whatever else are done by (semi)documented protocol over RS232, USB or Ethernet. 'Host' computer does not see empeg as a disk, but as another computer (which it is). Therefore, jemplode or any other similar empeg util will be of little use to you.
IIUC, Phat 'docking station' simply connects the 'Digital Media Storage' unit to the 'host' via USB. I gather that the station is not another computer, so the unit is connected as USB disk. If so, then in order to write your own 'phatman' you will first of all have to know how the things are stored on DMS (tune files naming, where metadata - tags - are stored, format of playlists etc). Next, you will either have to find USB disk driver for your Linux box (I don't know whether it is available or included in the distro), or figure out the low-level protocol USB disk drives use and write either driver or user-level transfer program yourself. Finally, everything should be dressed up in a usable user interface.
Depending on how much documentation is available to you (and your experience, obviously), this could range from interesting to very challenging. Good luck and keep us posted!
Cheers!
Dragi "Bonzi" Raos
Zagreb, Croatia
Q#5196, MkII#80000376, 18GB green
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Dragi "Bonzi" Raos
Q#5196
MkII #080000376, 18GB green
MkIIa #040103247, 60GB blue