MakerBot Industries

http://wiki.makerbot.com/cupcake-cnc-10:cupcake-y-stage-assembly

Read that part of the wiki again, and i think by watching the pictures you should see how its supposed to be assembled. The orange acrylic gets screwed on top of the wooden platform.
Makerbot industries was kind enough to give you a spare build platform. Thats why you have two of these wooden platforms and two of the orange acrylic parts (plus some magnets…)
I hope that clears it up for you.

For the Build Surface, you will only need the wood surface with "Build Platform" written on it, the orange acrylic surface, 6 M3 Bolts and Nuts, and your magnets. First thing you should do is determine which way you should insert the magnets into your build platform, the notches inside the piece of wood. You can determine this by placing the magnets over the Y-stage platform and seeing which way causes the magnets to join, you want to have your build platform stick to the Y-stage. Insert the magnets in so that they are sitting flush with the bottom of Build Platform. Add superglue to make sure those magnets stay in place….allow it to dry, and to make sure you didnt put the magnets in backwards, you should try and attach it to the Y-Stage. Next, lay the orange acrylic piece on top of the build platform. With the side with writing on top, insert the 6 bolts and seal with the 6 nuts. and there is your build platform all complete. Make sure the side with the rough surface of the acrylic is the one facing up. Pretty much just make sure all side wit writing are facing up and any writing is read normally, no mirrored/backwards.