Hey Ted!
Easy, just follow these steps. Open the Settings window and select the Events tab.
If it's a custom audio file (one that didn't come with the TD application), press the "new Sound" button. Press the Browse... button, locate the audio file and press Open. The TD should give it a name automatically. Just press OK and see that it is now in the Sound Library.
Press the "New Event" button. Select "Create a new event from scratch" and press OK. In the Description field give it a name/description. Set the Trigger to "The clock ticks". In the Conditions put:
isBreak and secondsLeft = 180
At the button, press the "New Action" button. Select "Play sound" and select your sound. Press OK. Then press OK again.
Done.