To manage 3 locomotives with 1 controller, you need to switch to DCC. In DCC, each locomotive has its own decoder so it responds only to commands sent to that decoder. A DCC control system (simple) costs between $60 and $150, depending on features. Decoders cost $15-$30 per locomotive plus labor if you have somebody else install them.
Conventional DC, which is what you have now, has no way to separate speed and direction signals between locomotives. So sections of track are separated electrically (called "blocks"). Each block has a toggle or other electrical switch to select which controller controls that particular block. The controller then sets the speed and direction for all locomotives located in that block. The ideal in block control is a separate controller for each locomotive, each connected to the blocks its particular locomotive is using. The remaining blocks are shut off, so any locomotives that are not being controlled are not receiving power.
hope this helps, but is probably not what you wanted to hear
