Region files are just a way for the program to assign the bases to regional areas for production and logistics planning.

When the game is initialized, the bases are assigned as they are read from the save file. This initial assignment is not optimal, so it is advised that you assign the regions on your own. There are two ways you can do it: manually, base-by-base; or by reading in a customized mapping file (and then manually adjusting, if needed).
After you edit or import regions, it's a good idea to exit WitPTracker AE and re-start it to be sure all of the by-region information is properly displayed.
Manual Method
The manual method is achieved through a combination of the Regions window and the Bases data set.
The Regions window can be displayed by selecting Regions... from the File menu. The window looks like this:
Selecting the New... button will show a window for specifying the name of a new region (up to 26 characters long).
To change the name of a region, select it in the table and then select the Edit... button, which will show a window for changing the name.
To merge two regions together, select the "receiving" region and then select the Merge... button, which will show a window to select which region to move from. This second region you selected will be removed and all of the bases currently assigned to it will be reassigned to the region selected in the Regions window.
To delete a region, select the region and then select the Delete button. If any bases are still assigned to this region, an error message will be shown and the region will not be deleted.
Select the Close button to close the Regions window.
Note that the Unassigned region can be renamed, but it can't be deleted.
The bases are then assigned to regions in the Bases data set. To perform the assignment, left-click the mouse in the Region cell of the base you want to edit. A drop-down menu will be shown as below:
Select the region you want this base to be part of from the menu and the screen and database will be updated. Repeat as much as necessary.
Import Method
The distribution of WitPTracker AE includes some base-to-region mapping files in the region-mappings directory. To import one of these files (or any file which may have the information you need), select Import Base-Region Definitions... from the File menu. You will then use the Open window dialog to find the file. Select the file and then the Open button; and then confirm to over-write the current definitions.
You can then fine-tune as needed, using the Manual Method, above.
Once you have a set of definitions you like, you can export them to a file for import for other games (and/or to share with your friends or opponents). To export, select Export Base-Region Definitions... from the File menu. Specify a location and name for the file to be created and select the Save button.