Get a copy of the Electrical section of the NSX service manual. There are links to .pdf versions in the NSX Wiki. At the back end of the electrical section, you will find wiring diagrams and one of those wiring diagrams will cover the NSX audio system. With a little studying of the diagram it will not be too hard to figure out what is going on. The diagrams have the wire color codes so it should be relatively easy to figure out which are signal, ground and power wires for the various channels.
If the amp in the trunk was a multi channel amp, then yes the signal lines to the door and sub amps have likely been 'intercepted' to provide the signal source to the aftermarket amp. You will likely have to pull the head unit out of the dash so that you can get eyes on the multi pin connection at the back of the head unit. With the aid of the service manual, you will be able to determine which of wires in the terminal block are the signal wires and then look for splices and / or non OEM wiring. The service manual sets out the procedure for removing the head unit without mangling things (hint - set aside a couple hours min if you have never done this before)
The section of the manual specific to the audio system has the pin outs for the terminal plugs which is going to be important because it will allow you to do end to end continuity checks on the wires (you will need a continuity tester). This will be important to find out whether the wire has been cut and spliced some where 'hidden'. I have attached the pin out for the plug at the back of the head unit. You can find similar diagrams for the door and sub units.