Can you post a pic?
Without seeing it, it sounds like the u-tube goes on the opposite side of the bulkhead. This is to ensure you maintain a syphon. WHat does the internal box look like?
To start the syphon, there are a couple of ways to do it. I use a piece of airline (clear tubing) and place it up inside the u-tube at the peak. Next put the u-tube in the overflow boxes-note both have to have enough water in them to fill the u-tube. Then you draw the air out of the u-tube with the air tubing. THis will draw the water up into the tube and when the water meets in the middle, pull the airline out(Don't drink the water by accident!!
)
Other folks fill the u-tube with water, then cover both ends with Seran wrap(cling wrap) and fasten it with rubber bands. Next they put it in the overflow, making sure both boxes have water in them, then remove the seran wrap. I have not tried this method. It kinda sounds clumsy. . .
HTH