i agree with george -- tank drain --> skimmer --> fuge/frag section --> return pump. assuming there's some sort of mechanical filter like a sock, pad, etc, catching bigger debris at the drain then the skimmer would be next at bat. this will help with less accumulation of gunk in the fuge/frag section.
i wouldn't worry about the pump and scwd chopping up the pods, they're so small most will make it thru fine.
question on the second drawing right where the water drains in, is that a pad which the water flows thru or is it solid bottom where the water drains to and over flows into the fuge section. if it's solid and that shallow, you will have a lot of splashes. assuming a 1" drain pipe and return rate of ~400-600 gph, you will end up with wet floor. something doesn't look right with that drawing.
with the first drawing, that corner section where the water drains in should have a sock incorporated in there to help catch bigger debris.
just a reminder of the skimmer section, check the
foot print of the skimmer
plus it's pump. better yet test fit them in place before glueing the baffles. also the return section, less than 5" is kinda tight, mag 9.5/ eheim 1262 just barely fits in there and if it touches any part of the tank or baffle, it can create a resonance that can be quite annoying.
with that drawing, the level of the water will be dictated by the height of the baffle just next to the return section. most skimmer for your size have a recommended water height around 8-10".
where is the sump going to be?....if it's underneath the stand, try putting the sump and the skimmer in with the tank in place(hopefully it's not filled). i have a 75 and a similar size sump, the only way i can get the sump and the skimmer in was to take the tank off the stand and come through the top. the middle support had to be removed and replace back. plus my skimmer now is a permanent fixture in that sump, there is not enough height clearance to remove the skimmer body.
what kind of lights are you planning to use in the frag/fuge section?
just my $0.02. hope this helps not hinders. don't want others to make the same mistakes i made.
good luck and have fun.