Baffles serve a couple purposes.
1 - They keep micro-bubbles from making it into the return pump area. This is not to say that they are needed, there's plenty of people who run their sumps without baffles.
2 - Maintain specific water depths in seperate chambers. If you look at the image I made on the first page, you see that the "Fuge" baffle is higher than the rest. The water level in the fuge area will be higher. Usually when you build a sump (I do anyways) that is going to have baffles, you figure the baffle height for the skimmer chamber based on the depth of water that the skimmer needs to operate.