The AC phone reps can book itineraries that aren't shown on the website, including those with segments on partner airlines. Just call in and give them the flight numbers. The price should be the same as what ITA Matrix (or Expedia) is giving you provided all the fare rules are met. I always try to book directly with AC because it is much easier to resolve any issues if the flights change. Right now with the MAX grounding, flight changes are the norm.

You can also Google ITA Powertools and try that.