Where will I have to clear customs from PUJ/YYZ/YHZ?

We are flying West Jet Halifax to Toronto and then connecting to Punta Cana. my concern is on the way back, we have to fly to Toronto then onto Halifax with only an hour connection time in Toronto. Will we clear customs in Halifax or in Toronto. I am thinking Toronto as it is the first port of entry.. But we were told our bags will be checked all the way to Halifax and wouldn't have to worry.. But i am worring... :S