The reason most biofilters are round is because the inlet pipe is designed to swirl the water in the bottom, which causes all the sediment to be pushed to the center, over the drain.
For the size of filter you are talking about, the swirl effect is probably not practical. My suggestion for building a bottom drain would be to lay out a grid of PVC pipe on the bottom, with holes drilled through the pipes so that you can easily drain the sediment out of the bottom from all the corners.
Of course, lovinglife's suggestion of a large bog filter would be much more maintenance-free, and would give you a nice area for a whole different type of plants and wildlife.