Copy a mission from CoD Steam folder to your CoD Documents\missions\single folder.
Open the mission in FMB.
Click group of aircraft you want to fly to select it.
Rightclick it and chose Properties.
On the 2nd tab (Group properties iirc) find weapons selection.
Open weapons menu.
Change loadout in it.
Save profile.
Now you can use this profile anywhere in the game hopefully. Or at least in FMB definitely.
To learn FMB basics check this site please.
http://www.il2-fullmissionbuilder.com/index.php