It can be done but not with the MPKMini template provided in S1. The premade template for MPKMini in S1 does not have all of the knobs available for use and they can't be added to the template.
I got them all to work by adding the MPK Mini as a New Keyboard device. You must delete the Device made with the template before creating the New Keyboard to avoid having a port conflict error. When you delete the device you will need to reset the Inputs to all tracks using the old device to the newly created device. Once added as a New Keyboard, go into a song, edit the external device, and put it into MIDI Learn mode.
Go to the MPK Mini and put it in to CC Mode, tap on the pads and you'll see them populate as knobs in the MIDI Learn screen. Switch to Bank B to add the next 8 pads. You can then change the knobs into toggle switches and rename the switches (e.g. A1-A8, B1-B8). Turn each of the knobs to populate them into the MIDI Learn screen and rename them to whatever you want (e.g. K1-K8).
You should now have all of the pads in both banks providing CC commands that can be mapped.