The DC commander should work fine but this board does not have cruise control. If you get the Cruise Commander instead, you will get cruise control (the board does cost 40 more). Both boards control lights, couplers, and smoke. I do not know much about MTH smoke units so I do not know if anything extra needs to be done to connect it to either board.
Either board works on both conventional or command. The board will auto detect the command signal when it powers up. If the Legacy/TMCC command base is on, powering up the engine it will go into command mode. If the command base is off, the engine will power up in conventional mode.
The program run switch is used to program the engine so it knows its ID and feature set.