Bubbles in your nail polish is never pretty, especially when you paid for a mani and you notice it later ..cry. The trick here is not to shake the bottle up and down, for that adds air to the lacquer; roll it back and forth between your hands. Rolling mixes the nail polish in addition, you are also heating it with your hands.
If your doing a home mani you want to let the first coat dry for a full five minutes, then apply the second, this will guarantee success! Just say NO to bubbles!