I have almost the exact same setup you are describing...a 5 gal fuge above a 30 gallon reeftank.
I drilled the 5 gallon with a bore-bit (I think this is the same as the butterfly bit described above). I drilled both a overflow and return and used Savko bulkheads (very reliable company)
http://www.savko.com/partlist.asp?pgid=2
Take David's advice on the wood backing when drilling the holes...and take your time...that thin acrylic likes to chip and break. Also consider painting on your backrgound before you get it all set up. There is special paint for acrylic...but regular old spray paint will work OK (be careful not to scratch it).
I used the 1" bulkhead w/ strainer for the overflow. Where the overflow enters the main tank I used a "J" pipe to eliminate any gurgling noise. I used a 1/2" bulhead w/ a barb fitting for the return.
Originally, I had appx 10lbs of small pieces of LR, halimeda, cheato (sp?), and red dragons breath algae. After two or three months I had zillions of pods in there and both the halimeda and cheato were growing well. It also works great for a grow out/frag tank for relatively
low light corals. I now have just a few pieces of LR (the rest has been sold off w/ attached frags) left and I am only using the cheato algae and I have almost zero algae in the main tank (that $#%!
bubble algae just wont give up). So I guess what Im saying is...build it...you'll love it
Good luck,
AEB