REEF2REEF Saltwater and Reef Aquarium Forum
I second #hybridazn recommendation. While some of the water in the skimmer section may not make it into the skimmer, the water will be returned to the main tank and mixed / diffused. I believe organics in water will diffuse itself fairly rapidly among other water molecules. Try not to think of it as x amount of water is getting no skimming and y amount is. The non-skimmed water will return to the tank, the nutrients will diffuse across the tank, part of that water will be taken into the skimmer and some won't. But the water will continue to mix and diffuse, so effectively all the water will be skimmed. There probably is some loss of efficiency from doing it this way, but I can't imagine it's significant.
And, if I'm way off base, please someone else chime in. I'm no expert on fluid dynamics or diffusion. I just stayed at a Holiday Inn last night.