MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
You could absolutely use pegs! I'd take a chopstick or a pencil and cut stubs from them. Then I'd glue one side, making a built in peg. Also, if you alternate which side the peg is glued to, it'll only for facing one way.