Im not sure how yours is set up. Mine has three sections. 1st is the skimmer area, second is the fuge, third is the return area. My baffles are the 3 glass design so it gets rid of bubbles. I think putting a filter in the first set of baffles would be okay, but not the area where the fuge empties into the return area, that would obviously trap them from getting to the display. In my previous post, DT refers to that stinky dead phytoplankton that your fuge critters love.