Assuming we're talking about this one: http://www.petsmart.com/product/inde...ductId=3523858
This can be submerged in up to 2 feet of water safely. That's about as far as you can go on "unrated depth equipment" but you can actually use a piece of hose to connect from the filter's output to the spray bar and just lay the filter near the bottom.
Most of the motor systems use in aquaria are epoxy-fill sealed assemblies. We call this "potting compound" in the real world. They assemble the unit in position then fill the entire casing around it with a low temperature kick resin epoxy. I have yet to find a brand of filter that doesn't seal their motors, the little flow switch on that one simply closes off some of the water flow and doesn't change the motor speed at all.
Remember to take that unit and clean it out in the sink every time you change the sponge cartridge, you can also buy a small "filter bag" and just put the filter inside it then tie the strings in a bow to reduce the rate at which the foam clogs.