I would recommend a couple of things.
First, you need to know if you want to make a true square or not. If so, you'll need to bake 3-4 layers depending upon the size of square you're using. I found I was making short, squatty cubes because I didn't have enough layers.
Secondly, if you are going to stack them askew on top of one another I recommend using a plastic separator plate or foam core. Cardboard tends to sag and gives a not-so-nice look.
Finally, make sure you dowel very, very well. You want to make sure the top square is supported on each corner (if applicable) and the center.
Hope this helps.
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