What do you mean crushed corals and poly filters? Is the crushed coral a substrate in the first section?
Is the ChemiPure and Purigen in bags, reactors, what?
Is the skimmer in the second compartment?
What is the pump for in the second section?
I had my skimmer (at least its output) in the first section so that any bubbles that may come out are handled before they get to the return pump.
Are you going to have a fuge?
Here is a pic of my fuge. You can see the drain from the tank and the return from the skimmer in the first section (far left). This skimmer is extermal so it sits right behind the sump. The middle section is a fuge that has oolite as a substrate and a heater. The last section houses all the pumps. Return pump to the display, pump to the skimmer, and the pump that runs the reactors (hanging on the back, returns to first section).
You can also see the auto top off on the right which has the sensor in the last section (where the pumps are) but fills in the first section.