Tips & Tricks to Demise of Nations Modding.
Editing the various-map images is possible using any standard imaging software including Photoshop, Gimp, Paint.Net. Please make sure to disable anti-aliasing while editing the image. Also make sure you store the image in RGB-mode (not indexed mode).
However, a pixel-editor rather than a photo-editor application is more suitable to edit those images. Pixel-editors to consider (in no special order):
The images you can supply to the bundle-maker supports images with tile-sizes of 2x2px and 1x1px. If you prefer to work with 1x1px/tile images, set the “format=1×1” in bundle.config.