Ben, are you going to have it flow Skimmer ==> Refugium ==> Return? If so, the outer baffles should be as high as the skimmer allows. 9" tends to work for most skimmers, but if you want it deeper then your skimmer will need to be elevated on a stand. Keep in mind if you do that, your skimmer may be so close to the top of the stand that you've got no way to remove and clean the collection cup.
The middle baffle can be as tall as you like it. In the 9" example, the center one is 9" too and simply lifted 1.5" off the base of the sump.