I think you have mis-understood how the BOSE amplifier connects to the RNS-E.
I have a 2004 B6 S4 with BOSE and RNS-E (was Symphony II).
The ONLY connections from the RNS-E to the BOSE amplifier are:
Left Front signal
Left Rear signal
Right Front signal
Right Rear signal
Note - NO sub woofer connections, the BOSE amplifier generates the sub-woofer drive signal itself from the 4 main signals.
The BOSE amplifier (on a B6 A4/S4 it's one amplifier for ALL speakers) is mounted in the right rear of the car by the fuel filler, and the sub-woofer is in the same place.
So if your sub-woofer is not working then the fault is either in the output connections from the BOSE amplifier or the connections to the sub-woofer - nothing to do with the RNS-E.
It's a pity you have sold your Concert II before completing the RNS-E install, it would have been useful for testing. You have changed 2 things - RNS-E for Concert II, and added BOSE. So fault finding will require more thought and care.
Sounds to me like you need the connections of the BOSE amplifier, NOT the connections of the RNS-E. I have that information on a PC at home and can PM them to you later today if that would help?