Well the thing with an overflow box is that both sides, the part in the tank and the part behind the tank have to be at the same height. Besides that, the pipe that connects the two can be as long as you want them to be because they work on gravity. So sure, you can still be able to use it to skim. Sounds like in the long run you may be better off if you make one, or at least 'modify' one to your own needs rather than buy something off the shelf just use it as is.
I have no experence making one, nor have I ever tried. But basicly it's pretty simple if you have a little practice in working with acrylic. It's two boxes connected with something waterproof to allow water movement between the two.