Unless it's one of the buffered Aion projects, you shouldn't need to connect the footswitch daughterboard in order to test the circuit. Note, however, that the daughterboard usually contains the polarity protection diode and one of the power filtering caps (in addition to the CLR and the LED). So, be sure about your power connections.
On the main board, try just the pads IN and OUT for the switch and the +V and GND for power. You won't be testing the LED, but you can still verify the circuit.