As a Canadian citizen, If I purchase a vehicle in the U.S. buy way of a trade in of my existing vehicle, will I pay GST + PST on the full purchase price or on the difference I pay?

You will pay duty and sales tax on your total purchase price. If you are thinking you are coming out with a good deal, not so, the duty you pay will take care of that.

I am wondering though, why you want to trade in down there, why not sell here and buy there. It sure would be less complicated regarding title and ownership and licensing.

I would suggest you call Ontario DMV if you do live in Ontario and find out exactly what a trade/purchase will entail south of the border.