You have to do each drive seperately, so I have a rule for each drive. Here are the ones I use for the Drive0 folder, just change the Drive0 to Drive1 to do the other drive on a dual drive Empeg.

The rules for the source Empeg have these options (This syncs the PC to the source Empeg):
Location1: E:\Empeg Backup\Drive0  (This is the PC)

Location2: 192.168.0.100/drive0 (This is the Source Empeg)
Only on Loc1 -- Delete from Loc1
Newer on Loc1 -- No Transfer
Same on Both -- No Transfer
Newer on Loc2 <- Loc1
Only on Loc2 <- Loc1

The rules for the destination Empeg have these options (This syncs the the destination Empeg to the PC):
Location1: E:\Empeg Backup\Drive0  (This is the PC)

Location2: 192.168.0.200/drive0 (This is the Backup Empeg)
Only on Loc1 -> Loc2
Newer on Loc1 -> Loc2
Same on Both -- No Transfer
Newer on Loc2 -- No Transfer
Only on Loc2 -- Delete from Loc2

When copying files to the Empeg, you'll have to issue a 'RW' command in order to write to the drives. You can do that through hyperterminal, with the WS_FTP client, or with CharcoalGray's web interface. You will not be able to write to the drives until that is done, so you could do a test run if you want to make sure things are correct before making any real changes. After you're done writing to the drives, issue a 'RO' command to put them back to read only mode.

If you want the destination Empeg to have any different configuration options (the name, IP address etc) then edit the 'config.ini' file on the PC located in 'E:\Empeg Backup\Drive0\var' with something that will save the config.ini in the proper Unix file format. Don't use NotePad, use something like TextPad or UltraEdit32.