I'm in the process of making a cake similar to this http://www.boobooska.com/sites/default/files/imagecache/grid-8/images/users/16/giant-cupcake-cake-with-polka-dots.jpg

I will be making a chocolate candy shell for the bottom portion of the cake. I plan on putting a cake board between the 8" cake and the bottom of the cupcake but I am concerned. I would like to put a central dowel through the entire cake (from the top of the cupcake to the bottom cake board)

But I want to know will that affect the candy shell when I insert the center dowel??? Will it cause cracking and mess up the support of the cake?

drill a hole in the center/bottom of the candy shell, so that when you insert the dowel, it just goes straight through cake.  Don't worry about making a hole just small enough for the dowel.....make it large enough so that there's no way you will miss it when poking down through the cakes.

Thanks for the input, I made the cake and completely forgot about pre-drilling a hole into the chocolate shell so I went ahead and sharpened a dowel rod, and put it through the cake like I normally do (with fingers crossed) and it went all the way through :-)