You can put a small plastic tray down that only covers a part of the floor-space of the tank, and build an undergravel filter with an airstone-powered uplift tube in it. Then you do the rest with soil or whatever organic based substrate you are looking at. This gives you added filtration (remember that an organic substrate IS a kind of filter, as are the plants that grow in it) with additional, active flow. The flow is really good for the plants as well.
Check out my journal for a more detailed description of how I did it, including drawings. It definitely works, very well. And my experience so far, at least with my tank, is that my system is extremely robust. I can dump huge amounts of food in there and add a couple bags of fish and pour in living water full of algae, etc, etc, and the tank parameters barely wiggle. Thats my tank, tho, which is 50 gallons, has a powerhead on the UGF, and heavily planted with well established plants.