Lots of things to think about here depending on how far out you want to plan. Aquascaping seems to impact flow patterns allot so I myself drew out several aquascape layouts in both the plan (Top down), and elevation (Side) views. I like having a few low in the tank to push crud off the bottom, and a few high in the tank to create ripple-like waves and high energy zones where my SPS are.
Are you running a closed loop? How bout a wavemaking device?
It's diffiucult to make general reccomendations on preceise placements since their are 50-ways to plumb the same tank depending how you set it up. Ultimately in a Bare-bottom tank you want to keep crud off the bottom and heading into the overflow.
Take some time to draw it out on paper several different ways. Include aquascape, outlet placement, and any impacts a wavemaking device would have if you are using one.
The intake holes going into a closed loop pump should be far enough under the water surface to not suck air (at least 6"). I placed mine about 14" below the surface and behine most of my aquascaping.