Instrument audio enters the audio interface, is converted to digital, passes through the rig, and is converted back for headphones, monitors, or a PA. MIDI and expression send commands; a MIDI cable does not carry guitar audio. Audio input/output and MIDI input are separate device selections.
The basic path is: instrument → interface input → ADC → digital input → Trim/EQ → pedals → digital output → DAC → headphones/PA. The interface's direct monitoring can add an unprocessed path that bypasses the effects. If a separate clean sound remains audible with a fully distorted preset, check direct monitoring and parallel dry paths before blaming the pedal.