[LSA]

...but I think I need to find where the the map files are stored that go into the QMB selection area.. Thats where I believe the order needs to be changed.

No, the order is set in [quick] section only. You just put exactly the same names as your desired maps folders (whether modded or not). Say, if your map folder named as My_Land_Map, then you should put My_Land_Map entry in the conf.ini as well