you can’t change between the main and alternative inputs. The way to get round it is to have a loop in one of the stomp slots (probably Stomp A) and plg the acoustic into the FX Return. This will activate the X retun as your acoustic input whenever you turn on the loop.
i sometimes use something similar with my piezo equipped guitars. I plug the magnetic pickups into the front input and the piezo into a loop. That way I can send the piezo straight to the ain outs using parallel path and send the magnetic pickups through the amp block etc.
This is actually a great idea, but it doesn't work anymore as soon as you start using the Stereo Monitor Out/Cab Off with the classic KPA models.
The Direct Out is used for the right channel and thus you're not able to use any loop functions.
A workaround would be to get the ability to switch to/mix in the return jack with some kind a new loop stomp.