They will be selectable in a drop-down box from your profile.
I need one government member from each sanctioned alliance to PM me with the image that their alliance wants to use. These images may be a maximum size of 150x48.
Any new Sanctioned Alliance must wait 10 days to get their image added here (the same amount of time required to get your flag added in-game). Whenever an alliance replaces another as sanctioned, the old alliance's image will be removed when the new one's is added.
Edit: Don't forget that the background here isn't white, so it would be a good idea to make sure that any images submitted have transparent backgrounds.