I have never poured ganache over two tiers before.. only 1, and I was wondering what advise anyone might have about doing this. What is the best way?? I would assume I would stack the two and then pour??

Depends on the look you are going for. If you want drips down the side of the top cake and the top of the bottom completly covered, i would pour ganache on the bottom cake, then stack. In this cake, I poured over the bottom one, stacked, then poured over the top.