This falls under the category: I wish I had known that before I booked... so I am sharing this info.
If you book a flight on Air Canada with United Miles you will not be able to access Air Canada's website to choose seats or check-in online, etc. You also will not be able to pay extra to upgrade to AC's version of an economy plus seat, even by calling them directly. You can call and obtain an Air Canada confirmation number once booked, as I did with my Swiss International ticket and my Lufthansa ticket but unlike Swiss International/Lufthasa websites that allow access to website features with their airlines' specific confirmation number, if you did not book with Air Canada you cannot access website features- even with an AC confirmation number in hand.
I'm sharing this info because while I appreciate the ability to book on alliance partners with United miles, I wish I had known about this quirk of Air Canada flights booked with alliance miles before booking. I would have chosen differently, probably purchasing tickets on direct flights instead. Hope this helps others out there considering using their United miles to book award travel on Air Canada.