When wanting a high output setup you can just re-feed the stock and then any audio wiring would be independent. So just re-land the stock alternator cable on the HO alt then you run separate alt wiring for the sound system to the extra batteries.
You could also disassemble the stock terminal, add a new terminal on the larger battery, then run a wire jumper from the stock feed to the new battery terminal. This assumes the new battery terminal has multiple outputs.
Note that you should have fusing on any wiring added to the batteries or alt.