You can do either the one or the other (it's configurable through the SMUFF.cfg file on the SD-Card, as stated here https://github.com/technik-gegg/SMuFF/wiki/Configuration-file-(SMuFF.cfg)).
Since it's utilizing Bondtech gears, I recommend direct bowden. In this case, the SMUFF doesn't control the feeder, only the revolver and the selector. The feeder is supposed to be controlled through the E1/2 stepper of your mainboard.
Some sample configurations can be found here: https://github.com/technik-gegg/SMuFF-Ifc