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Go to a glass store and ask them to cut you some glass. I tried Lowes glass and it was way too thin and it cracked. Just look in the yellow pages under glass.
just what they said i did too in my 20 gallon. 1/4" HD acrylic either GE 100% silicone (make sure it doesn't have like mold lock or else its no good) or aquarium silicone. You could get glass but its nice having the acrylic laying around for future things, and not sure but it could be more expensive.
This is what they looked like when finished. I have since added one more baffle which is an "under" between the return section and the refugium to act as a bubble trap. I also have an inhabitant in the refugium now.....a PJ that was getting picked on by my Royal Dottyback. There is lots of flow through the refugium but it is so gentle that the PJ is quite happy down there.