I don't use secondary groups in Xenforo. Though Brogan says that all members primary user group should be registered, it isn't feasible for me in Xenforo currently due to:
1) My forums uses rank images (pip icons/w.e). So instead of a title for a rank, we use images. Currently Xenforo doesn't support images for that.
2) To achieve what I want I have to use <xen if> tags in the user post bit, and and have new groups for every rank. The rank icon doesn't show up if the user is in a secondary group.
3) If I add the images via acp as user title for that group, I'd have to disallow custom user titles for members. I don't want to do that, I allow certain user groups to edit their user title and if I have a image there the image will be removed after a edit of custom user title. So that option is ruled out.
Due to these reasons, secondary groups are completely useless for my forums. I just hope that the group promotions coming for 1.1 promotes from group to group rather than adding the promoted group to secondary.
So at least for me, primary groups is being used and not secondary