If you buy a package, your tickets will automatically be coded onto your KTTW cards (unless you ask them to be on separate cards).
If you have tickets from a broker, or AAA, or the Disney Store, you will have to take them to the Lobby Concierge desk after you check in, and they can be added to your KTTW cards there.
But mention to the CM who checks you in that you want to have your tickets coded onto your KTTW card, just in case there has been a change in procedure since the last time I did it. Procedures at the check in desks change once in a while; perhaps some day they will be able to code tickets onto your KTTW cards as you check in and save you the trip to the Lobby Concierge desk.