As far as i know, footswitch is true bypass. Meaning, if its set to bypass mode, the signal will go from the input directly to the output of pedalshield, thus there is no need for software programming.
yes, as nik said it is true bypass, meaning that when the effect is off or bypassed the guitar signal goes straight from input to output.
The pin7 of the DUE will "feel" when the 3pdt footswitch is activated or not, the pin will be high when the effect is not working and low when is on.
You can have a look at this for more info: www.electrosmash.com/forum/pedalshield-u...shooting?lang=en#535