Hey Knasser,
what you have to do to achieve this is setting the LFO to modulate the Filter in the ModMatrix and then holding one of the freely assignable round buttons on top of the matrix down while pressing that field in the matrix, where you just set up that modulation. This will create a voltage controlled modulation depth for this connection and you can then set aftertouch to modulate that newly created column.
This is one of the MxBs strongest features, especially since the extra slots since 2.0.