Do I just put dowels in the bottom level of the cake? Do I need to cut holes in the cake boards for the central dowel that goes through the whole cake? What are the best type of cake boards to use? Do I put the dowels in before I cover with fondant of after? If I use a central dowel all the way through the cake what is the best way to cover it at the top because my decorations will be standing on the top of the cake. I know so many questions but I really want to get this right! Thanks a bunch! 
Corrugated cardboard boards are best.
You put dowels in each layer that is supporting another layer (i.e all layers but the top one).
To insert a central dowel rod, you don't need to cut holes in the boards before hand. Just sharpen the end of the dowel and push it through (or hammer) all the layers.
Put the dowels in after you cover it with fondant.
Cover the top hole made by the central dowel with buttercream or hide with flowers.
If you want to use the central dowel all the way through, measure so it it is slightly shorted than whole cake is going to be. put it in prior to putting on your top tier. Tht tier would need a hole in it for the dowel, but you just silde it into place over the dowel, so that you don't have a hole through the top.
I don't always (usually) use a central dowel. Jsut ones between tiers.
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