Yes. That is exactly what I want. Students typically look at courses in the order that they take them. Yet because AP starts with an "a", those classes are coming first.

I concur.  We are in the process of moving to K-12 and I decided to try out the system by entering all of the course requests in the On Suite.  I spent a good chunk of my morning arranging the classes in a meaningful sequence to facilitate the course request process only to discover that the sort order has no bearing outside the departmental listing.  It does not make sense for AP English III to be listed before English I when students are selecting their courses.  An order based upon the progression of the classes within a department seems (to me, anyway) to be the logical order of the list.  And since I took the time to create the aforementioned order, I would love to see it elsewhere.