You can do as described. You might also be able to set up your booking with you BAEC number so you can choose seats, but then switch to MP before you travel.

But what you can do is get a booking agent to set different values for FFP status and value. This means your status will be correctly profiled for the entire trip.

Usually the FFP fields FQTV (FFP to credit for value) and FQTS (FFP to use for status) are the same, but assuming you put your MP number into the booking, a reservation or customer service rep with the relevant training would be able to put your BAEC number into FQTS giving you all the status benefits automatically but allowing you credit back to MP.

Hope that's useful.