Being aware of your heat level is indeed practice. It worked a lot better over time. I overheated quite often at the beginning and much lesser at the "end". Mostly I overheat when I don't know the mechanics of the boss to 100%, e.g. keep firing while dodging some attacks and overheat because of that. You have to watch your heat level a lot but it gets better and knowing the mechanics of an encounter also helps a lot.