You are opening up the proverbial can of worms with that question. There really is no "best" method. Everybody does it a bit different it really depends on your tank, setup, aesthetics and so on.
Some might tell you to drill and plumb it through the back with a bulk head or even split it and put two holes in the back or you can keep it super simple and just run a U over the top and have it return in the tank. Just keep this in mind, the longer and higher you run the plumbing the less flow you get at the end.
Mine will be running up through the over-flow, then split so I have dual returns in the tank to help increase and even out the flow.