Ok. Redesign... well kind of...
I found where I had see the first section with a "dead zone" and in fact it isn't so since the intakes will be below the mechanical that will sit in section "1".
The basic idea I am "borrowing" can be seen here:

Here is an overall shot with my auto-water change solution (not my idea, just my implementation).
So water will come into section "1" and through a filter sock, then up through ceramic rings (mechanical).
The water overflows into section "2" that will be populated with foam or scrubbies or something else?
Water will go up through section "3" that will have the Eheim substrate pro.
Then some water into section "4" that will have the polishing pads and some over section "4", both leading to section "5".
Return via the pumps.
Auto-Water change
I will have an auto-drip system adding about 2.25 GPH to the tank which will add the entire tank size every week (i.e. 380 gallons a week). This will result in the filer to overflow, but I have a bulkhead at some level in the filter that will drain water to a holding tub with a traditional sump pump in it. When the water level in the holding tank gets high enough, the pump ejects the water to a drain.
So, what do you think?
I have thought that if I want the bio media (Eheim substrate pro) to be wet but not submerged, I could eliminate section "1" and enlarge section "5". Is that better?