It will really help you if you:
a) do not book tickets on Air France while logged into your Flying Blue account if your intention is not to collect miles for those flights in Flying Blue; and
b) add the intended FFP and number where you want to bank the miles to the booking while you are making the booking (either on the AF website, or via a travel agent or third party website).

Be warned that in Alaska's programme, you cannot earn in the cheapest discount economy fares - so if you end up booking travel in these classes, you should instead use your FB number

http://www.alaskaair.com/content/mil...ir-france.aspx