I just checked. JNB is still an add on like other TATL flights. So you can select the seat for free during booking for you and companion in the same reservation. Just click on the seat and it should assign it. Now any connecting flight to/from the ATL-JNB flight will require waiting for system to upgrade you. As long as there's upgrade space available you get it right away. Note that if there's only one upgrade space it'll skip you and go to the reservation with only one.