Take the similar sized thin cake card as the one that's holding the top cake and place it on the base cake. Make light marks around the card to show where the top cake is going to sit.
Take one of the dowels and plunge it into the base cake gently, about an inch from the edge of the circle. Keep it straight
Take the pencil and mark the height of the cake on the dowel.
Now break the the dowel off by snapping it at the mark. Sometimes, it helps to just mark the pencil line with a knife to provide a "give" point.
Repeat with remainder dowels making a square inside the circle mark.