First you have to decide what you want to keep. What fish, what corals? When you decide that, you can settle on one of the two tanks. You don't need to drill a hole in the tank.
Your coral choices will dictate what lighting you will need. Some corals need stronger lighting than others.
If you are sticking with the 30, you can get by without a protein skimmer, but I would definitely have one on the 55.
I have seen successful reef tanks(small ones) with simple HOB
filters as the only mechanical filtration.
Tell us what tank you are going to end up with and then we'll give you lighting and filtration ideas.