The major benefit to having your fuge above the tank is that it wil allow your pods
to make it to the tank without having to pass through a return pump. That gives them a better chance of surviving. I haven't drilled a tank either but I know it can be done. Have you thought about using an acrylic tank, they are much easier to drill?
Also, you will need to light the fuge and you will want your flow to be low have the drain on one end of the tank and the water flow in on the other. That will maximize your macro filtration.