If you don't maintain a consistent skimmer level you're going to be constantly adjusting it the skimmer. The height of the baffles are up to you. The key is to keep the water level in the return zone lower than the baffle for the skimmer zone.
Here is a picture of my current sump. It's not great, but it shows how the water level stays consistent in the skimmer zone.
Actually, now that I'm looking at it, the levels are really close and the upright is blocking the view of the baffle. Either way, the water level is lower now in my fuge and return section, but the water level in the skimmer remains that height.