As soon as your raid team runs in and the first mobs spawn, click Start or Next. This will begin a timer, highlight the current wave in green, and the upcoming wave in red. A chime will alert you one minute before each wave.
If a wave spawns before the timer thinks it should, manually tap Next to force the timer to move ahead.
If at any point the timer moves ahead to the next wave, but it hasn't actually spawned yet, just hit Pause to stop the timer. Once mobs spawn, hit Resume to get back on track.
In the unfortunate event of a wipe, hit Stop to reset everything back to the beginning.
The entire event is just under 180 minutes in length. Good luck!
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