If your using it to transfer your wort from the mashtun to your boil kettle, what i do is run a gallon or so into a pitcher first to set the grain bed and remove most of the loose grain/husks, then connect my pump. You need a valve on the output of the pump to control flow, set this so that you only get a slight trickle of wort at first. Pump this back to the top of your mashtun and open the valve just a bit more. You don't want to run it wide open as it will suck the grain bed down so tight that nothing will pass thru it. I run it this way until the wort is clear and then move the hose to my boil kettle and drain. No grain gets thru this way.
Now if you use it for whirlpooling, then I know that my pump will just push hops (pellet hops) right thru the pump without clogging. Don't run the pump when you add hopps, but run it after they break up. I don't know about flower hops, never used them with my pump.