OK, here's one answer. Two parts, one of which may answer your question..
First, if you're going by boat. To check in, we've gone to Bedwall Harbour on So Pender Isle and phoned the "proper authorities" from the dock. It's their phone and I don't know for sure to whom it's connected. They will give you a number which you can treasure whilst in Canada. There may be other places, but I'm not aware of those.
Second, If you're driving up, at the end of I-5, in Blane you'll cross the border. Just after you cross the border there's a big building between the roadways that contains Canadian customs/immigration/touring/etc. On the left going north. Stop there and you can get a permit for the boat. You will end up with a small slip of paper. We still have ours from 2009.
When we entered Canada at Sault St. Marie, Ontario, pulling the boat, they just waved us through with no question, paperwork or number. No-one ever asked us for anything for the whole summer.
As far as I know there is no check out, just report to the American authorities. By boat: Friday Harbor, Anacortes, Port Angeles. By car, at the border crossing. They will NOT ask to see any paperwork from Canada (to our knowledge.)
One word of caution. No smiling, jokes or random comments. Even if you are talking to a turbaned Sikh who speaks impeccable English. They are there to do business. You can admit you don't quite know what to do, and they'll be very helpful, but no jokes.
Boris