Thanks again for taking your time to help me through, I really appreciate it.
Ive taken a look through the code and tried to understand whats really going on.
What kind of "mix" does he use? What is a mix? 
I assume he has several mixes that each one output a sound.
 if (digitalRead (note1button) == LOW) {
1.  if (note1playing == 0) // if key is pressed and note is not started
2.  {
3.   note1playing = 1; // set note flag to playing
4.   note1end = micros() + note1time; // capture time to make note change state
5.   digitalWrite (note1pin, (1-note1state)); // start the note at high level (replace the write with something faster)
6.  }
7.  if (note1playing == 1){ // if key is pressed and note is already playing
8.   if (micros()>=note1end){ // see if its time to change note state
9.    note1end = note1end + note1time; // set time for next change
10.    digitalWrite (note1pin, 1-note1state); // change the note state (1->0, 0->1)
   }
  }
 }
If we take a look at this part of the code.
Line 4 and 9 = Keeps track for how long we have been holding down the button.
Line 5 and 10 = This is the part where we make the output sound, and also the part that is confusing me a bit. He uses his "mix" here with the opamp, but I cannot see where he really output the specific tone.
I hope Im not making myself look dumb or something.
Cheers