Actually the bottom of the filter has some big holes drilled on it so water enters by the bottom aswell, however yor suggestion is good I had to find the way to rise the gravel as you said.
And filter do work pretty well, actually it is working as the only filter system for a 5" flower horn who is in a 55 gal, water is crystal clear.
Cheers.
You could cut a sponge to fit. Like an aqua clear one which would act like a prefilter. I did that with a much simpler pvc filter that has only two stages. It has a sponge filter and then some biomax. But i also have an aqua clear on the tank as well.

