I figured it out myself.
1. Use the Rate Scaling dropdown to divide the system clock to a lower rate. I'm using the F28069; it starts at 90MHz.
2. Use Up/Down count mode to get an additional divide by 2.
3. Choose a Timer Period that gives 50Hz (14046 for F28069)
The final PWM rate == sys clock/ rate scaling / period
If Count Mode is Up/Down, there is an additional divide by 2
Note that the current frequency is displayed next ot the Timer Period entry
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