I have made several tiered cakes and am having a problem with the dowel rods coming up through the top tier. Am i not stacking correctly? Can someone please help me with this dilemma? Thank you.

When I stack a cake I use bubble tea straws. When you go to stack it stick the straws down in the cake, and cut it level with the frosting. Stack and repeat with all tiers, then put one long dowel through the whole thing cut slightly shorter than your cake. Patch up the whole and you're done. I don't know what dowels would be sticking out of a cake...

Have you seen any of Sharon Zambito's (sugarshack) videos? She has one called succesful stacking, it'll teach you everything you need to know about stacking, plus some.
http://www.sugaredproductions.com/product/Successful-Stacking-DVD/

Are you talking about a dowel going all the way through from top to bottom to keep the cakes in place during transport? Or the series of dowels in the different layers? If it is the series of dowels to support the different layers, you don't need any in the top tier unless placing them to support a heavy topper. This shows how to dowel. http://www.wilton.com/cakes/tiered-cakes/stacked-tiered-cake-construction.cfm. Of course each cake is already on its own cake cardboard which doesn't really show up on the pictures.

I also don't understand how the dowels can be coming up into the top tier, unless you're stacking without any plates or cake boards.

Ditto. There aren't any dowels in the top tier. There's no reason for them.

You might want to try SPS. It's easy to use anyway.

If you explain exactly what you do, it might help people with their answers.