The four teams playing in the first four are in the last two at large slots. They get placed in the bracket wherever that belongs. That changes from year to year based on how highly seeded some of the one bid league teams are. For example, in a typical year the CUSA winner might be seeded below the last at large teams. This year, with Florida Atlantic certainly getting a better seed than those teams, those teams move a spot further down the list. In other years, the top team in the MVC might be better than the last at large team, but this year's MVC winner, Drake, is probably not. So they go below the at large teams.
So it just depends on where the individual teams that make it end up. There isn't any "template" or something that says that the last at large teams should be 11s or 12s or, really, anything. They go where they "belong".