My Prodigy has three boost settings (B1, B2, B3), plus the normal non-boost setting (B0). There is a boost button to cycle through the settings. The boost settings are programmed to adjust the aggressiveness of the brakes. Higher boost settings apply a higher starting voltage and provide higher voltage for the same rate of deceleration.
I used the thumb wheel to set the MAXIMUM output for the controller. This is independent of the boost. I set it such that the trailer, on gravel, will barely lock up the wheels; it won't lock up on packed gravel or pavement.
I usually leave it on the B1 setting. It provides the best feeling for both highway and city towing. If I'm towing where I need more brakes on the trailer (i.e. wet/slick roads) I set the boost higher. If I need less trailer brakes, I set the boost lower (only done a few times when the trailer brakes felt really aggressive).
Another feature I use on my controller is the reverse function. When stopped with foot on the brake pedal, I press and hold the boost button for 5 seconds until the display shows "r". This disengages the trailer brakes for a couple of minutes so I can back up slowly without the trailer brakes dragging. Especially useful to back up my sloped driveway!