Hole placement is based on live rock structure and size of tank. One of my main objectives with placement is to provide the most random flow possible, while exchanging alot of water from bottom to top of the tank. Also, you need to keep the intakes (you will have to put screens on them) accessible to be readily cleaned, so that sometimes limits placement options.
Best loops I have seen typically draw from lower in the tank (usually on the back behind live rock piles) and either emerge near the top or aim up and forward at a slight angle.
As for a wavemaker, you cannot use them with real pumps, however, I have 3 loops on my system and 2 of those are on appliance timers that turn them on and off. One is on during daylight hours (12 hours) and one alternates on and off each hour. It does wear on the pump to be turned on and off alot though.
Wade