Depending on the state of the IT integration between AC and AF, AC may even give you a boarding pass on the AF flight. With your seat assignment and Skyteam program FFP number encoded if that was part of your reservation. So you shouldn't check in for the AF flight separately online prior to presenting yourself to the AC check-in counter.

Make sure you have a piece of printed documentation that has a ticket number prefixed with 057, AF's ticket stock code. Assuming you bought it from AF. A mere PNR locator may not be good enough.

Marketing alliances don't matter for interlining.