For starters look at Kevin Watson's excellent repository of FRC code and FAQ's.
http://www.kevin.org/frc/
Specifically for the EDU Controller read the encoder_readme.txt within the zip on how to make the code work with the EDU controller.
http://www.kevin.org/frc/frc_encoder.zip
Now if I remember correctly digital ports 3 through 6 are designed to interrupt on both the rising and falling edge. So if you connect your clicker to one of those it will trigger an interrupt on 0,1,0,1,0 and so on. Simply remove the "Phase B" logic and it should work as you need.