I would do my best to remove the air bubble, or one tube. If you have 2 tubes, you're only flowing have the water you would be with 1 tube, so the flow is slower. As water falls into the overflow box, it splashes and creates bubbles. With a single tube, the water is moving fast enough to carry the bubbles down the tube without them getting stuck at the top. With 2 tubes and the slower flow, the bubbles can build up and eventually break the siphon. The idea with the powerhead is another one that would work, but is unnecessary IMO if the overflow is set up correctly.
Since I have set up my overflow box, I have not lost siphon unless I was cleaning the box or working on plumbing and physically lifted the tube up, and there is no accumulation of bubbles at the top of my tube with 600+ gph running through it.