I'm a big fan of filling bottles from the faucet: turn off gas to keg, bleed most of the pressure through the release valve, purge bottle with CO2 from extra outlet on manifold, fill at an angle straight from tap, and cap on foam.
I fill all my competition bottles this way, and it works very well. I usually don't lose more than an ounce or two of beer throughout the whole process.
I have perlick faucets with removable spouts, and I remove and sanitize them before bottling.