Hi Mate,
It's all explained in the Deneb manual:
http://www.e3b.de/usb/soft/dnb_manual.pdf
Rescue jumper is for first time install, this is because the software is located inside the flash and you can install the USB stack and Lucifern from the new drive that will be mounted after booting.
After you installed the software you should switch off your Amiga and then remove the rescue jumper, now your hardware is ready to use as intended.
You should update the USB stack to 4.4 as that's the latest (inside the flash of Deneb I believe resides 4.0)
The FlashRom can also contain romable modules, you can clear these or add others using Lucifern, I assume there is some documentation that accompanies Lucifern, again I suggest you read this although I found the GUI easy enough to use, everything was self explanatory.
The first time you run Lucifern it will save any modules you have re-kicked like OS3.9 BB's, that's a pretty cool feature as you can then put them in the Deneb Flash Rom and disable the OS update/reboot.
Good luck and remember
'read the manual!'
