Couple good reasons mentioned above for putting skimmer in your first section. Sometimes those darn mini bubbles get pulled into your main pump and go right into your tank.
+1 skimmer first. No reason to seperate rock and refugium really other than takes up space from the chaeto. Make sure first section is large enough to fit whatever skimmer you'll get. With the extra space you could also pile rock in there. Big thing would be just 3rd section only needs to be large enough for return pump. Then set it off with 3 plates to create a baffle. Can stuff that with filter stuff to cut out on any bubble problems or larger stuff from escaping into pump area.
+1. Can achieve baffle effect by being creative and keeping your sump without baffles. Great way to go if you don't have specific final outcome in mind on your first sump, as you will end up playing and changing things. With baffles, this will be more complicated.
I run a 2 chamber sump, if nothing else to keep my water level exactly where I want it for my skimmer. I run my ato on my apex, so there is a fluction of water level in the return chamber between times the ato runs.
well the sump was pre planned for the tank lots of baffles i bought it from a forum member good plan out im just trying to get info there are pics of it listed in my tank build thread for the 75 gallon.