In Logic Pro X, I instantiate Filtryg on an Instrument Track in order to enable MIDI input from my controller keyboard. Then, in Filtryg's plugin window, I select the audio track I want to effect in the "Side-Chain" drop down menu.
After routing the audio, make sure that the little square keyboard buttons are enabled in Filtryg itself, anywhere you want to have the MIDI notes act as a modulation. They can be set to modulate filter cutoff, envelope times and LFO frequencies directly (keytracking), or the note triggers can be used to launch envelopes, as well as reset LFOs to their starting phase (using the buttons with the vertical lines).
Since Logic's "Side-Chain" input is being used to route to Filtryg's main audio input, it appears that running a secondary audio route to Filtryg's side chain input is not possible while MIDI control is enabled. Side chaining is still possible if Filtryg is instantiated directly on the audio track being effected, but that disables MIDI control. If anyone knows a good way around this, let us know.