yes, you are running it backwards. If you listen and add the rubble rock around the dump pipe, I usually run the pvc to the bottom and put a 90 on the bottom. Then the water has to flow through the rubble. the add the live rock or make a refugium in the middle chamber. your baffles look a little close together, but the idea is to create the flow through this area and the baffle give the air a place to escape...Of course if your flow is tremendous then you may have to back down your pump. You may also have a little break in period simaliar to a skimmer.
Vince