You should consider more than two holes. A single intake and then a few outlets are good.
They can move a lot of water. If you use something like an Oceans Motion, then they can be nice and random. Being higher pressure, they can really move a lot of water... especially if you use some eductors in the tank. They are also usually pretty quiet.
Buy bulkheads that are threaded on the tank size. If you need to repair something, you unthread your strainer on the intake and loc-line on the outlet and thread in some plugs... they don't have to be seal 100% for a few hours of work, but with some teflon tape, they usually seal pretty well even just being hand tight.
You have to be careful not to use too large of plumbing on the outlets. Velocity is good, not water that barely moves. I like 3/4. If you move up to 1" the same amount of water comes out, but but slower... if you use 1.5", then it is a trickle.
Closed loops are great in larger tanks. Kinda hard and waste in larger tanks. I have a 12x4x3 planned and I am going to use a AmpMaster in the 6500gph range with a 4 way oceans motion with 3/4" outlets on each 6 foot section (so two of these). Also have a Tunze 6200 with Sea Sweep on each side. This is as efficient and cheap as I can do it. On a tank like this, a MP60 fizzes out into nothingness pretty quickly and the flow gets really weak and I don't want to have them all over the place - Tunze 6200 is a little stronger, but still need a whole bunch of them. The Oceans Motion 4 way can move water like 8 feet and blow sand away from the glass with ease. People just don't know how much more flow this is unless you do it.