Fyi I just recently flew on a ticket upgraded with the buy-up offer online. The FCM buyup was purchased a few days after the initial ticket. The additional MQDs posted as a separate line of activity for each buy-up segment. MQM bonus posted as 'Seat Upgrade: 50% MQM Bonus' in the normal ticket activity.
Odd thing was one segment posted with the 50% bonus and the other didn't. Sent a tweet and it was resolved quickly and the bonus posted.