You should get the pick up hose all the way to the bottom of the tank. If you use the fuel pick up for the engine, you will miss the worst of it. A fuel pick up typically does not go to the bottom of the tank precisely to avoid picking up crud that has settled to the bottom.
I'm not at the boat but I do have a walbro pump that works well. It moves a gallon per hour through the filter and back to the tank. Mine was set up with a dedicated line to the bottom of the tank and the return line dumps at the top of the tank.
Do you have an access port you can open? It would provide you the ability to stir the contents and better allow the stuff to be sucked into the polisher intake.