ok so i was thinking about it for a bit (its 1:30 at night) at first i was thinking run the plumbing from one side into the first locline then continue down, but then the ball valve would stick way out in the back of the aquarium, and we dont want that because that takes up to much space. then i got stuck and the remember that you wanted to have the ball valves in there for possibly 2 things, one to control how much flow and 2 to close them if needed. not really sure if this works for closing them, but just get those things that go on the loclines that you can turn, im sure after a while you wont mess with them here is a link to show what im talking about, not to many options here, just an idea.
the name is ball valve there are a bunch that are different for whatever you want.
http://www.bulkreefsupply.com/Plumbi..._36/index.html