Your FB numbers needs to be the main number in the booking. However if you are logged in to any Skymiles account on the website or app, then Delta will automatically put that number in instead.

Basically if you wish to earn with Flying Blue you will have to logout on the Delta website (And do not open any itineraries on the delta website while logged in), as well as the app. This does reduce the functionality of both platforms somewhat. In the end the question that you should probably ask is if it is worth collecting with Flying Blue, or if it would not be easier/faster to do so with Skymiles. Especially if you are based in the US it may actually be easier to gain status with Skymiles.