Just before US left Star Alliance I booked a ticket with US Dividend miles that included Jazz and AC mainline segments. Couldn't select seats online for the Jazz segments but had no issues with mainline (and Rouge when the route was switched). It's typically a hassle though when the ticketing airline is not AC.

I recently booked an international PY itinerary through Expedia that includes both Jazz and mainline. No issues at all with seat selection, nor with upgrading the resulting domestic B fare segments.

While it's not perfect, I have actually had decent success using the AC seat selection tool for tickets purchased away from AC.com.