From my own personal experiences, you can't really add the res folder into the jar file unless you use InputStreams (this is so that the game can read the res files inside the jar file and not in the same folder), however, you can add the native files into the jar.
With JarSplice, there is a tab called "Add Natives," you use that tab to locate the natives you want to add to your game (i.e. windows, mac, linux native files):
Under 'Add Natives', add your native files for the specified Operating System, in this case I'm adding window natives.
For adding res files, I would recommend to have them in the same folder as the game, but if you use InputStreams to fetch the resource files, than the following will most likely work:
Under the tab "Add Jars," add the jar of your game and for your assets, add them as a .zip file (I used WinRar to create the .zip), here's an example:
This way the game fetches the resource files within the jar file and not within the folder it is in.
Hopefully this will help you.