In the MODS folder for the hi-res add-on, include a folder called Scenarios. In that folder include the actual scenario files for the DG, with the adjusted POS and headings. JSGME will switch them in when you load the mod, and should replace them with the originals when you switch it out.
Many add-on and modified bases alter the Earth.cfg and Earth/Base.cfg config files. These files are used by all bases, so using JSGME can cause problems when using it to manage base add-ons, especially if you use it to manage more than one at a time.
The best thing is to see if the add-on base comes with a Config/Earth.cfg file. if it does, compare that to the original Earth.cfg file. The most common differences are adding observer points, and adding/modifying VOR transmitters. You can manually add the new observer points or VOR stations to the original Earth.cfg, then remove the add-ons Earth.cfg from the MODS folder.
The Config/Base.cfg file is usually modified by add-on bases. The common difference is that the add-on's Base.cfg will have additional textures listed. Simply cut and paste the additional textures to the original Base.cfg, and delete the Base.cfg from the MODS folder. You'll be loading a few extra small textures used for buildings, runways, etc, but that shouldn't cause any problems, or affect your framerate noticably.
Everything else (such as the hi-res surface textures that can affect framerates) are handled in the specific base's config file, and will be switched in and out by JSGME.
