If the tank is glass then I recommend glass baffles (at least 1/4" thick, 1/8" is very brittle). You can use silicone. They say that some varieties of GE silicone is safe, but I only used the stuff I could get in a large tube from my LFS.
You need to know how big of a footprint your equipment will have before you put in the glass. I would put your skimmer in the intake section and make it as small as you can but still be able to easily get the skimmer and anything else in and out. I did put a one-way bubble trap here into my live rock/chaeto section (basically the water falls down, then exits into the middle section on the bottom. I think have another bubble trap into my return that is also one-way (exits at the bottom).
Leave at most 1" at the bottom of the bubble trap. Any more than that and you'll get bubbles going through.
I also did a 55g sump and I think my return section ended up being around 14". I wanted a larger return section to help with water changes. I can drain 7 gallons before getting to the point of starving the return pump.
For the glass, I went to a local glass shop. They cut all the baffles for me. I don't remember exactly how wide I made the glass, but it was 1/4" less than the width of the glass inside the tank. I think I paid $5-$6 per baffle. You can use acrilic but I'm told the silicone doesn't stick as good to it.
