Can I decide what frequent flyer number I want to earn Miles on after I have checked in or travelled?

No. You must decide which programme you wish to earn Miles on at the time of reservation or check-in for Qualifying Flights and at the time of paying for other qualifying goods or services. No changes can be made to the membership number once a member has checked-in for the first flight of an itinerary.

Related questions

Do Family Bonus members have to travel with the principal Family Bonus account holder?
Can I earn Miles on domestic travel within Australia?
Do I earn the same Miles Accelerator bonus if I have purchased a Skywards Flex or Skywards Saver fare?