Yeah, when the bar(s) are full is when your auto-attack will fire off.
So what you want to try and do is time your combat arts and spells so that they are not in the middle of casting when the bar fills up or else your auto-attack will be delayed until it's done. So basically what you are doing is using your abilities while the bar is filling up, it'll feel a little wonky at first, and your dps will probably go down some while you are adjusting your timing, but once you do have it down so that your abilities aren't delaying your auto-attacks you will see a sizable increase in your DPS
