I would make absolutely sure the FF scheme you wish to credit to is in your boarding pass. In fact I would change it today in the AY or QR site then check on QF. I have one booking I need to phone up and query as it shows both BA and QF on the Qantas.com site.

Lounges and checkin will provide you with access access based on your higher status card. It takes some extra clicks in the system to ensure the right program is charged for lounge entry. (Yes on occasion I have met some lounge agents with a different view...)

Then on leaving the lounge, I check again that the only FF number is the one I wish to credit to and they cannot see the other one anywhere.

I know it may sound pedantic but these systems have an annoying habit of not updating correctly, and trying to get miles credited when you have the FF number on a BP of the wrong program and you need to manually chase miles, is so painful I cannot be bothered anymore.

KF