Here are few things you should know to ensure miles credit to BMI properly.
If you are elite with UA, even just a Premier Associate, you should use your Mileage Plus number to make your reservations because you can select Economy Plus seat. After your are done with ur seat selections, call United Airline to change your number to British diamond club number. After they changed the number, check your online receipt again to see how many FFP number is on the reservation because some UA agent will add your BD number, but forget to delete your UA number. If this is the case, your miles may or may not credit to BMI account even your BD number showed on ur boarding pass later
If you have luggage to check or have pending upgrade with UA, then you need to check in with your UA number first, then ask Gate/RCC agent to change to BD number after u drop ur bag/upgrade cleared. If you use Confirmed Regional Upgrade or System wide upgrade and is cleared, you can switch to BD number anytime.
Don't use Easy Checkin Machine to change your Number unless your flight has no connections because Easy checkin will simply ADD BD number to the record without deleting UA number, some flight segments will still credit to UA even BD number is showing on the Boarding pass.
If the miles ever post to your UA account even with BD number on the boarding pass and you want to recredit to BMI account, you need to call UA to remove mileage credit first, then follow the standard missing miles credit request procedures on BMI website. If your boarding pass shows UA account number, then you can not recredit back to BD, at least not without a significant effort.
For all other *Alliance Flight, you can give your BD number at the time of reservation because there is no Economy plus or luggage issue(except US). If for some reason, you need to add number at check in, make sure to tell Check in Agent enter BD xxxxxxx, lots of agent don't even know BMI is *A partner and airline code for BMI.