I don't think you can. From what I can gather, you need to upload to $800000-$802000 in order for the Jaguar BIOS to decrypt the ROM, and the Skunk prevents writing to these memory areas due to the demands of a handful of people trying to control the Jaguar community to prevent piracy of roms.
Of course, I may be wrong (I do hope I am) and it is possible. Maybe kskunk can answer this?
I think there is no way around the situation. I checked deeper and there is only one memory chip on the board so the Skunk BIOS must reside at those addresses, and they are blocked from writing to prevent the BIOS from being overwritten and bricking the board.
Does the Atari Flash Cart allow testing of encrypted code? It appears to have a completely independent ROM for the BIOS.
If worst comes to worst I can yank the Skunk Flash Chip and install my own preprogrammed chip as a last resort.