If your flight originated in Canada and you have a boarding pass for a connecting flight to a U.S. destination, you must follow the U.S. Connections signs, go through pre-boarding screening checkpoint “C”, and then go through U.S. Customs and Border Protection. There's no need to worry about your checked luggage.
Note, however, that U.S. customs officers are authorized to recall your luggage, if necessary, for manual inspection. If the customs officers do not yet have the information on your luggage at hand, you will be asked to proceed to the waiting area.
