Missions fill in from the top-left corner, with the most recent first.
If you do a banner of 12 missions, they will line up properly, but your last line of mission badges won't fill a full line (since they don't at the moment either).
Basically, your badge list will look the same, but with the banner above it, similar to this:
If it bothers you that the end of your list isn't aligned properly, then you can do more missions before you start the banner.
Also, as mentioned by udondan, if you redo a mission then that moves it to the start of your list. So if you did the banner missions, then redo 4 of the missions you'd already done (which would move them ahead of your banner), then 2 new missions, then everything would be aligned perfectly: your banner would be lined up, and your bottom row would be full.