When I finger, thumb or pick what I'm playing I'll mute using my left pinky and index finger behind it. So if Im playing a riff and I wanna include a mute after hitting the 5th fret on A, relax your hand so your not fretting the note, and keep your ring finger around the third fret. This will help mute any harmonics you might otherwise hear.
That being said, when slapping I mute with my entire left hand laying across the neck and plucking with my right hand using either my index or middle finger.
I hope this is comprehensive
