Controlling two Atik motorized filter wheels is easy, only problem is a few wires must go from the Main port to the Exp one, so the controller can read the signals from the filter wheel.

The wiring is quite clear in the following diagram:

Once done, you can control both wheels with a single controller, using both "Filter Wheel" and "Filter Wheel EXP" programs.

If you want to see an actual wiring done (only for one wheel, but to get an idea), take a look here.