What a coincidence. I just came on here to ask a similar question. I'm planning on booking a UA flight with the first segment on Air Canada. I guess the answer for me, before I even ask the question, is to not check in on AC right away (the first flight will be a Dash 8 on a really short flight, so it's not like there's any benefit to early seat selection), then once I'm within 24 hours on the UA flight, select a E+ seat on ua.com, then check in?