As others have pointed out, either during booking or after booking you simply need to input your United frequent flyer number and all the benefits should pop up. The reason why you can't book Air Canada domestic flights on United's website is the same reason why you can't book Lufthansa domestic tickets on their website or Air New Zealand domestic tickets on their website. It would be one thing if those sectors were connecting flights which had UA operated flights or the sectors were flights to/from the US for which United has a JV with the airline, but this is certainly not the case for strictly domestic itineraries.

UA Plus Points are only valid for flights operated by United Airlines, Lufthansa or ANA metal. Complimentary Premier Upgrades are only available for flights operated by United Airlines. Priority Seating including complimentary Economy+ Seating is only available on flights operated by United Airlines. In terms of the actual benefits you'll get as a 1K flying Air Canada they would include access to the Air Canada Maple Leaf Lounges at the airports you are flying out of (provided they have them), additional baggage allowance, priority boarding (Zone 2), security and check-in (follow signs for Star Gold).

Lastly, does it make sense to credit points to Aeroplan? It depends. If you are flying enough within Canada it could potentially make sense. For instance, if you are spending $3000 CAD in a year on Air Canada flights and you fly roughly 25,000 miles on Flex tickets, then you would earn 25K which would give you upgrade credits you could use on future AC flights. But generally, I'd second what the others say and simply selected United as your frequent flyer program during booking on the Air Canada website, at the airport (if you haven't enter the UA details into the site) or over the phone. You'll have all the Star Gold benefits from being 1K (including IRROPs protection), accrue miles to MilagePlus which I find happens to be the best program for upgrades in the US too.

-RooFlyer88