I am in a similar situation (AA Emerald), and I always book BA flights using my Blue EC account, and immediately change my FF number to AA (for Avios bookings I use Finnair to do this). The advantage is that my booking inherits all my personal information (including seat preference) and all my BA flights are listed on the EC page.

I have not booked an HBO flight recently, but changing the FF number should not affect seat preference.