If you're shipping in two seperate boxes, you can not use the same Paypal label twice. You need to pay for postage twice.
From Canada Post's point of view, they don't care if they're from the same purchase. You purchasing their services to ship two boxes, so it would only make sense to pay twice.
In my opinion, calculate what will be cheaper: 2 seperate boxes or together in the same box. Use the Canada Post website to estimate dimensions and weight for the two scenarios and see what will be cheaper.