Yes; you can. I do it all the time and have never had a problem. I will often fly, for instance, LHR-YYZ-IAH, check in with my CDN passport since that's what I used to enter the UK, then use my US passport to clear customs in YYZ. Both passports are attached to my NEXUS/ GE account so perhaps that's why it's so easy. If I overnight in YYZ, then I just show my US passport when checking in the next day. Nobody seems to mind, or even notice the switch.