You are definitely doing this the hard way. Per page 41, use the bypass mode with any of the analog inputs.
In the Marantz, tell it to send your LFE signal to the L and R outputs OR use both of the sub's inputs so it can receive the LFE from the Marantz via one channel and the integrated via the other. This would let you hook up the sub to both the integrated and HT receiver.
Even if you could find something that had digital outputs for just 2 channels of the HT I know of no situation where the digital input also bypasses the volume control.