Using a milk crate in your kayak is definitely useful for keeping all of your gear in one place while on the water. However, sometimes even that crate can get disorganized.
Do you have an old license plate laying around? Grab a drill and some zipties, because you have an easy-to-install separator. The pictures below explain this mod pretty well. Just drill some holes around the edge of the plate and ziptie it to your crate. As you can see, I put mine in place to hold 4 Plano boxes to one side and my random loose gear on the other.