Substrate covering LR question

I posted a while back explaining how we had placed a PVC conduit system
beneath and behind the LR, and placed a rio 2100 feeding water through the
conduit system thus sending water flow through the LR from the inside out.
The PVC system runs down the middle of the tank and covers an area approx.
32X6"
Our 55 gal is set-up to view from both sides, so the LR is arranged across
the center length of the tank w/ space between the LR and glass on 3 sides
of the tank. It is piled up against the overflow box on 1 end.
After arranging the LR, we placed our crushed coral substrate around the LR
building it up against the sides of the LR to a depth of 3-4" throughout.
In some places the substrate covers 2-3" or so of the side of the LR and
some has seeped under and between the LR spaces down into the area below the
substrate level to the PVC waterflow system.
Some LR has been repositioned and now sits partially on top of substrate.
The water flow is good through the LR from the rio 2100.

Getting to my question:

Should we be concerned that problem areas can form where substrate is under
the LR?

Should we be concerned that flow through portions of the substrate could
break up problem areas later down the road?

Are the areas where the sides of the LR are covered vulnerable to problems?

We believe that water flow through the PVC system should permeate through
the substrate under the LR to the outside edges of the LR and keep those
areas flowing. We didn't originally plan to cover as much of the sides of
the LR, but we wanted more depth in our substrate. It also makes the LR look
more natural against the bottom.

Any comments?

Thanx.

Mark and A

[snip]
Getting to my question:

Should we be concerned that problem areas can form where substrate is
under
the LR?
[/snip]
With CC substrate or similiar will need to clean or do small vacuum. Reason
= It trap nitrate within it curvices.Your substrate critter (like worm) may
not unable to get through to release it.

[snip]

Should we be concerned that flow through portions of the substrate could
break up problem areas later down the road?

Are the areas where the sides of the LR are covered vulnerable to
problems?

We believe that water flow through the PVC system should permeate through
the substrate under the LR to the outside edges of the LR and keep those
areas flowing. We didn't originally plan to cover as much of the sides of
the LR, but we wanted more depth in our substrate. It also makes the LR
look
more natural against the bottom.
[/snip]
Any coarse substrate will trap decay if not taken care by scanvenger or
janitoral crew to get rid of. In due time, the decay will release more
nutrient to your tank. End result, = ALGAE = built-up and problem. With
fine sugar size substrate, worm or any critter live under the sand will
distrub and clean those sand. While the sand being distrub and clean, it
will also release any gas that is trapped.

CapFusion,...