If you are using a siphon box you should add an airline check valve on the top of the U tube so you can manually remove air bubbles or have it on a constant suction from a venturi on a powerhead or use a Tom Aqua Lifter water pump.
Having a strong flow through the U tube will help minimize bubbles. Limiting the overflow to a maximum of two U tubes will help keep velocity high and discourage the formation of air bubbles.
The outer box should have a standpipe that regulates the water level and keep the siphon primed when the return pump stops.
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