I like to put the very tip of the tubing in the receiving vessel (the bottling bucet) at the very bottom. Then, I "curl" it so when the cider/wine/beer enters, it "swirls" around and fills from the bottom. This works fine for me. But if you're really worried, you can sanitize a long handled spoon and gently stir. I've never stirred and I've had good results.
Broken Leg Brewery
Giving beer a leg to stand on since 2006