Ask at checkin. Go to the desk and explain to the check-in agent what you want.

However, be warned that there are numerous reports here of people changing from FB to another programme, but the miles still post to Flying Blue anyway.

If you're uncertain where you want to post miles for a ticket, it would be a better idea not to enter any FFP details (and, therefore, not to log in to the relevant airline's website while making the booking) so that you retain the ability to add the FFP number at the time of your choosing (ahead of departure, during check-in, or even by doing a retroclaim after having flown without any FFP associated with the booking)