This is a VL set and the dual sound systems are meant to be run as a unit as they have very different, but co-ordinated, sound sets. The rear facing unit can run on its own but the sound set won’t be right. Together they do rumble around very nicely.
You are right that programming the engines as one is not obvious from the first couple of pages of the manual. It is however in the instruction video Lionel did at the time - probably because they put two orange modules in the box, one for each engine, when you are only meant to use the lead engine one. My UP version came with two modules separately numbered for the two units but the second one, whatever info it contains, is not used.
More generally, programming most Legacy A-A diesel sets under one number isn’t always obvious from the manuals, which contain standard Legacy instructions about assigning separate engine IDs and building a train. But it seems that they all default to running as a unit out of the box and you just program them with the same ID and they maintain the default setting. Or at least this is what I have found with all the A-A sets I have.
