The EPR transition is excited by broadcasting through a coil. We scan across a frequency to find the transition, and then lock to that transisition.
Exciting the EPR transition depolarizes the alkali metal (Rb, for simplicity). Once the alkali metal depolarizes, it begins to repolarize. In the process of polarization (another, different 5 minute lesson), a certain frequency of light is produced. We can track the amount of light produced as a function of frequency. Technically, we look at the derivative and lock to the minimum of the derivative (so, a maxima or minima, but we know it's the local maximum), using a feedback loop.
Once the frequency is locked, the AFP sweep can begin. At the moment of resonance, all the spins flip. If the flip occurs in a well-behaved manner, the feedback system can track the transistion and the system is locked to the new EPR transition. In this state, the 
He spins are pointed opposite the direction that the alkali metals are polarizing, so a return flip is required.