I have an order for a fondant cake with beer cans in the middle as supports. It'll be a square flag on the bottom with a round cake on top of the cans. Has anyone ever done anything like this before? I'm not sure how to put the cans on the cake so that they don't sink in once I place the other cake on top of them. Should I put a dowl under each can? or a dowel and a plate under the cans? Any input would be great!

I would not put a dowel under each can. Since the cans are separate from each other they will wobble and make the cake unstable. I would get a round cylinder about the size of the can or a little bit larger that has a flat top and put the can on that. You will have to cut out a hole in the cake to set the cylinder in. The top cake which will have a separator plate under it can sit on top of the cans. The feet of the separator plate can sit into holes that you put in the top of the beer cans. This will help it from sliding. I would also stack on site.

Here's a helpful thread:
http://cakecentral.com/cake-decorating-ftopict-738323.html

I would just cut a hole in the top and bottom of each can and insert push-in pillars.

Some subterfuge is called for here. Stack and support the bottom cake as you usually would, but cut a hole in the bottom of the cans directly under the hole you drink from so that the dowel runs straight through the can,through the cake board, and up through the upper cake.

Maybe a piece of PVC or VERY thick (1" of bigger) dowel the exact length of the can through the can? The bottom of the can would have to be cut off. The legs of the upper separator plate can go in the drinking hole. You can glue the can to the bottom separator plate.