You download the Arduino development application, download the game code from GitHub, open it up in the Arduino software and you are looking at the code. USB connect an Arduino Mega and upload the code into it. So from there you need to modify the code to use your alternative sound source, the WavTrigger.
The WavTrigger you insert a SDcard loaded with your sound effects and/or music. The WavTrigger only uses uncompressed CD quality wav files. The BSOS code has been designed to send commands to the WavTrigger to have it play individual tracks, start, stop, pause, loop, set volume, etc.
If programming is new to you this would seem a bit overwhelming. That is where I started from, not a programmer, but slowly figured it out and rewrote Eight Ball that is now being played by people.