THe skimmer goes in the section all the way to the left. The baffles is 9"s in height, I have an Octopus skimmer which is best suited for 8"-9"s of water. I have filled it and there are no leaks. The section all the way to the right is the return section. I took the basic design from a well known Brand that you do find in the LFS from time to time.The build looks nice. Clean lines.
Have you filled it yet? The single baffle on the left in the pix appears higher than the triple baffle. That is not good. I'm guessing your water level in the chamber all the way on the right is as high as the single baffle on the left. That probably throws off the water level for your skimmer (if it goes in the chamber on the right, which I suspect it does).
The height of the single left baffle should be the same height as the inside baffle of the triple baffle configuration.
Hope this was clear.
Russ