I used to wash them in the dishwasher...takes forever, and I would get food crud stuck in the bottles. At that point I would rinse with star san and let bottles drain. After about 25 gallons of bottling, I got a keg set up...screw bottling. Now the only time I bottle is when I fill from a keg...
If you don't have a hydro...get one. If you don't have one, I would wait until the air lock is bubbling only once every 2 min. That is what I used to do before I started getting all technical with my gravities.
Like previously stated... just fill keg with co2 and release the pressure valve...