Your diagram shows a very different setup. I can't find a flow diagram for my specific tank but it is not like yours. The way mine is setup there is always a direct source of water for the pump that does not even involve the filtration. Of course the flow is going to go with the least resistance.
I would need to pretty much tear everything down to see where the first and second in/out happens to be... Hmmm, I suppose I could just pull the sponges and feel for the transfer point.
One thing I've noticed is that if I just use the air risers for the UG filtration I can see bubbles coming up through the back sponge filter. If I go through the built in only I see nothing in the sponge area. Even though under powered I think that my under gravel is doing the better job.
I am thinking about plugging the inlet that goes directly to the pump cavity and enlarging the inlet for the sponge intake. That MIGHT make the built in filtration system a little bit effective but there would still be the issue of the free overflow between the carbon/ceramic to pump sections. I think it is just a bad design.
Here is what I am thinking. I'm going to add another Whisper 40 air pump and run each full blown to each riser. Plug the water intake in the built in pump chamber and replace the current 264
GPH pump with a 100
GPH pump. This would give me a strong UG filter with also pulling enough water through the ceramics to mayhaps allow a secondary bacteria level.
I know that I MAY be put down for what I'm thinking but I know and understand UG filtration and the built in system makes zero sense to me. I want to maintain flow through the built in but just don't trust the setup.
Sigh, I would LOVE to cut out the plate between the main tank and filtration area and increase the usable tank size but am afraid that it may be a structural support panel. I'd hate to remove and have the tank blow out.
If you want I can use your above flow diagram and modify to show the difference but I think the filtration on my tank is just poorly designed. I mean how can you have filtration when there is always a direct connection from the input to the output pump?