I just fired up the DAW to check I am not imagining things. I switched on the A-PRO and the LPK-25 but left the S61 off.
In stand alone Komplete Kontrol responds to both keyboards. You have to make sure the synthe in KK is on the same channel as the keyboards, or set to Omni.
In Sonar the synth in KK responds to both keyboards. The arpeggiator and chord functions work.
You do not have to select the keyboard in the Komplete Kontrol controller menu. KK just responds to MIDI like any other soft synth and passes it on to what ever is loaded. What you don't get is the mapping of the encoders and the browser functions etc.