I have recently been using the Kemper with two guitars - an electric and an acoustic.
I created a patch in the normal way for the electric, and I created a special 'Acoustic' Performance slot with a mono FX loop in the Stomp A position (with no Amplifier/Cabinet enabled).
I ran the electric into the main input on the front and the acoustic into the FX return.
This worked very well. The only problem I had was that the Tuner would not allow me to tune the acoustic. It appears to take its feed from the Input jack only.
I'm not sure the best way to do it, but what I needed was an option to allow the Tuner to be fed by the FX Return.
Or maybe we just need an option to allow the FX return to be used as a Secondary input, or maybe even better, if the 'Alternate input' could be used at the same time as the Main Input, but with an option to choose which one to use, selectable per Performance slot, if the hardware allows.