just position the air line so that the Co2 bubbles freely get sucked into the intake of the filter. I usually position it about and inch or more directly below the intake. I've pulled a vacuum on a 2 liter bottle before by having the hose directly into the intake and it collapsed the bottle. Luckily it didn't pull the mixture through the hose.
Okay, so basically the same thing that I did with my filter intake, I used a bit with the diameter of the air tubing and drilled and just pushed the tube through. I'll have to look at it when ever I get the filter.