My understanding is the DCS Commander Remote (that comes with the starter sets) will operate any DCS engine (that has the factory default settings.. i.e., that hasn't had its ID # changed via a "regular" DCS system).
And no, I don't think you can customize a DCS Commander Remote to work with a specific engine.
Think of the DCS Commander Remote as basically a "conventional" transformer control that's wireless (& has a few more buttons that allow for access to PS2/3 features... but NOT including running multiple trains independently on the same electical block).
If you want to run two engines independently of each other, they'll need to be on separate electrical blocks, and the receiver for each block should be at different points of the layout (farther away from each other the better). That way you can point the remote at the receiver for "loop A" and run that train, and point the remote at the receiver for "loop B" and run that train.
