Hey man! How are those corals doing I traded you? Never heard back from ya.
As far as sump stuff goes, its going to depend on what you want to do!
Personally, I wanted the largest refugium I could get, so I made sure I had enough room for my skimmer in the skimmer section, made sure there was just enough room for my return pump in the return section, and dedicated the rest to my refugium.

Having said that, I only had a 20g tall to work with, so space was TIGHT. You will have tons more room with the 55g.
I did a middle return just because it allowed me to have a bigger and deeper refugium on one side with my skimmer section on the other. I think a complete flow through may be a bit better for the chaeto, but I also don't think its a huge deal.
Just my opinions and experience, though.
Brandon