Ringtones in the iPhone are treated like Music and Videos. So if you want to manually manage the music and the movies you keep on your iPhone, while keeping synchronized all your ringtones… you can’t.
So if you want to, you’ll need to manually manage your ringtones as well.
To activate manual management, go to your device in iTunes, in the Summary tab under Options you’ll find a checkbox named “Manually manage music and videos”.
As you see ringtones are not mentioned, but that actually is the case, so the checkbox should say “Manually manage music, videos and ringtones”. :)