You don't want any opening for air at the full carboy. It won't transfer the wine it will just suck air. Yes, the wine will churn in the receiving carboy until the wine covers the bottom of the tube. I use a long tube just so the wine will cover the end faster. If you have a way of adjusting the amount of vacuum you may wish to turn it down to some level that it is not churning vigorously but still moving at a decent rate of transfer.
Thanks Mike. I may have miscommunicated my question. I have a vacuum all the way back to the full carboy. It's the full carboy that I'm wondering about. Do you leave the little extra opening so air can fill the carboy as the wine leaves it?
And while you are pulling the wine into the new carboy, will it churn vigorously while filling it?