Bonnie is a real pain in the @!%$, as his A.I. level is equal to 17 in the custom night menu. You just need to check the hall lights often. This same method can be used for stopping Chica. He usally begins moving early, around 12:15. Checking the cameras is pointless, as he can disable them as he moves.
Bonnie, seen with Chica and Freddy.
Bonnie right outside the Office.
Bonnie's jumpscare (one you have seen enough times)