Hacking PWM and ADC

I'm working on a project in my Electrical Engineering class at Ocupational Skills Center, and require a little help understanding how to "reinvent the wheel", so to speak. The project in question is to make a arduino controlled guitar effect, I've seen it done a couple places, but I have trouble seeing what they are doing specifically in their code. I understand WHAT they are doing in a basic sense, as in that they are directly controlling the PWM pins and ARC, but I'm having trouble finding many resources on how to do this. I've found the page on this site on using PWM, but I'm still unsure. Could anyone share some resources that I could study for this?

What I'm trying to emulate: ElectroSmash - pedalSHIELD UNO Arduino Guitar Pedal.

The link is to an open source project. They give you the Arduino code and the circuit diagram, so all you have to do is build it. They even explain what all the parts do (the Arduino just acts as a volume control that you adjust with two buttons).

What is your real question?