gglave, I'm not sure what you are referring to by online check-in with AC -- if I have a seat assigment by phone, then the UA check-in agent will give me an AC boarding pass at SFO, right? (In which case I don't actually have to check in with AC, I can just go to the gate.) Or are you saying that AC will not give me a seat assignment by phone in advance?
I'm referring to using online-check in (also known as "web check in") on your computer 24 hours before your flight to enter your passport information, select better seats if they're available, enter your contact information for flight-delay text-messages etc. and print our your boarding passes.
Then you just proceed to the luggage drop-off stations at the airport and then head to security.
If you check in online you're also greatly reducing the chance that you'll be bumped.
United online check-in should be able to produce you both your United and Air Canada boarding passes, but if not you can check in separately - Once at United.com and once at AirCanada.com. Start with United.
https://www.united.com/web/en-US/con...necheckin.aspx
https://www.united.com/travel/checkin/start.aspx
http://www.aircanada.com/en/travelin...eller/checkin/
For your trip home, most hotels have computers and printers available for guest use to check you in.