It is up to the host software to route MIDI from the keyboard, touchpad and pitch/mod stick. Automap Universal does not control the host software directly, and so does not change MIDI input routing. Sometimes this is not even desirable - perhaps you want to stab some chords in one synth while tweaking the filter in another.

The default setting for these controls is 'USB a' in the Automap templates. Make sure that the first ReMOTE SL MIDI Port is selected in your host software and as the MIDI input for the MIDI track that you want the keyboard to play.