I've interlined between UA/AC, and US/AC when the flights are on different tickets. I don't think you'll have a problem but make sure you have detailed itinerary with you because the check-in person won't be able to see your later flights so you need to give her exact flight numbers, and times. I know this sounds obvious, but I usually go to the airport expecting them to be able to see everything, so I thought I'd mention it.