DocumentMap is using the order of report structure to create the tree. For the moment, the only way to change this order is using "Bring To Front/Send To Back" in report designer, which is badly named in this case, and awkward to use.

You should:
-add Bring Forward/Bring Backward functions
-document in DocumentMap help section that theses functions will also change the order in the report structure.

Ideally, a move up/down in report explorer view would be even better (and more intuitive).