Mavericks+: (Desktop Wallpaper) How can I use both the Apple Desktop Pictures and a local folder?
You can move your wallpapers into /Library/Desktop Pictures/ and have them in single location. This shouldn’t affect the system because I have the wallpapers since Leopard and each OS update only include more wallpapers.

Go ahead and include yours in there. Make sure you make a backup of /Library/Desktop Pictures/ just in case you want to revert them back to default state.