My son has been crying it out. He falls asleep in crib in about half an hour but all night he has random quick breaths like he can't calm down. 6month?

Don't worry. Assuming he is otherwise healthy (not having a cold or cough or bronchiolitis) then don't worry about it. He is probably just going in and out of a deep sleep. When he breathes quickly he is probably waking up very briefly. We all have very brief awakenings especially during rem sleep.
Crying it out. Children who cry themselves to sleep will frequently have sigh breaths even after they are asleep. There is no right way or wrong way to teach a child to go to sleep at night. 6 month olds are comforted by being around their caregivers. Your son is obviously upset. Eventually he will stop crying but i question if that is the best way to promote attachment and security.