Properly written templates or other mods will have all their files organized in the correct folder structure, so all you need to do is drop the /includes/ (and in this case /admin/) folder into place and all the files will land in their correct places. Most will be in the override structure so that they don't wipe out any existing files, but some in admin may need to overwrite the original copies of files. All the rest of the files will be unaffected.