I would try fix the channeling in the MBBR. You really need the whole thing to work like the active side.
If you want suggestions, send me a PM.
I agree with JKB. Optimum would be your air and media coming up the center middle and the media going back down the sides.
Also, I would put a lid on top of your mbbr tank to keep light out with just maybe a crack facing away from the light to allow C02 to escape. (I cut my tops off the blue tanks where they narrow just below the top with a reciprocating saw. Then you can just flip the lid over and it fits perfectly as a removable lid.) Nitrobactors (the ones that convert nitrite to nitrates) will work much better in the dark. Actually the nitrosomonas (the ones that convert ammonia to nitrites) don't like light either. In reality there are lot of other species but you get the drift. Ultraviolet will actually kill them if it's sufficient.
The above two things can make a difference when your fish load increases.
I'm guessing you're using a couple of airstones in the bottom of the mbbr tank?
I'll see if I can find a picture of a barrel with an airstone set up on aquaponics nation that I thought was pretty clever.
Here it is:
