We just went through a similar experience with our US purchased boat. It was registered in the US (I think the US calls it "documented"). We had to undocument the boat in the US, then import
it to Canada. This is when we payed the tax (13% in our case).
In the recent past, when a used boat
was privately purchased in Ontario
(and I assume BC), you only had to pay the provincial sales tax. I'm guessing you now have to pay the full HST, but it might be worth inquiring. In the past, when we licensed our boat, we were sent an invoice for the PST.
Boats in Canada must be licensed or registered. Registration is federal, licensing is provincial. Licensing is free (at least in Ontario) and does not have to be renewed. I think registration costs $250, and must be renewed every three years.
Transport Canada Registration site
Registration allows you to carry the vessel name and port of registry, whereas licensing requires that you show your license
number. Otherwise there is no other functional difference as long as you remain in home waters. Not sure how it affects international travel.
One question I do have is whether registration is better/essential for international travel. We have licensed so far, but will likely register this year.