i would use glass for the baffles, its pretty easy to score and snap. you only need peices 12" wide so it should be pretty easy to find peices already the right width. the main question is the hight. are you going to use a skimmer? that will be the first desision you need to make, the skimmer you choose will ditermin the size of your first chamber. it needs to be large enough to fit the skimmer and also the correct depth for the skimmer. most skimmers will need between 6-8 inches of water depth to work best. your particular skimmer will determin if you cut your baffles shorter to allow for the correct depth or if you need to raise your skimmer off the bottom by building a box or somthing. you may end up making 3 baffles 12"x10". the first peice will go against the bottom forming your first chamber, the next will be raised off the bottom somewhat and forward of your first baffle an inch or so. this forms the bubble trap. if you want your second chamber to be a refugium decide on a sand depth, 6"? 4" i would cut the first baffle for your fuge area a few inches over the depth of the sand. you dont want to go up all the way as this can make the water swirl over the edge and constanly stir the sand. you can always use eggcrate to make the walls taller to keep cheato in its place. same for you last chamber, keep the wall short and use egg crate. the last chamber holds your return pump and if the water tumbles over the edge it will make a ton of bubbles that gets returned to the tank.
kinda how i set up my 10 gallon sump