Well, Im rather opinionated about closed loops..so take it with a grain...
The intakes should be as close to the surface as possible w/o every being exposed to air in case the sump turns off (and the tank's water level drops). This is for easy cleaning, as well as keeping the CL pump clean. Simply, more dirt gets tossed around near the bottom...and unless you plan to use an inline sediment filter with your closed loop, it will just gunk up your pump. The other main reason has to do with keeping the intake clean. Close to the top means it is way easier to notice and reach in and clean. Down far, behind rocks and corals, maybe even out of possible view, means that the intake wont get cleaned as much, and might even get looked over...causing problems. And on a side note, a closed loop should either have a very long intake strainer (rather hard to hide so most prefer the little black ones mentioned next), or if you are using the standard rainbow plastics type...two or more intakes. This allows critters more flexibility when getting close to the intakes. Otherwise, a snail on your intake would not only get sucked in, but as its being sucked in, the water suction would increase that much more...killing it. I like at least 2 intakes...so if a snail clogs one, the water pressure wont increase as much and simply come from the other intake.
And I know the question always comes up...why not run the CL off the overflow? Well, you can...ONLY if you have a very large overflow box....and usually isnt worth it then. See, if the sump pump is turned off, you need enough water in the overflow box to maintain the closed loop. That means you need a standpipe and the sump overflow to be above the closed loop intake...otherwise the CL would run dry. Not only that, but the height between the two intakes (CL below, Overflow above) must be enough to maintain a water volume large enough to maintain the CL if the CL pump were to turn off and then on again while the sump was off (think about it while the sump is off, turn off CL if it feeds from the overflow that means that the level in the overflow will rise...going down the overflow drain to the sump...CL comes back on and doesnt have enough water to run). And then what about evaporation? The overflow box needs to function as your new sump pretty much...too much hassle for most to bother running the CL through the overflow.