Muting with the thumb?

I'm a bit confused about the proper way to hold the guitar, especially for chords with muted low strings, such as A and D. I've read that you should keep your thumb on the back of the neck for proper technique, but I've also seen people mute the E and/or A strings with their thumbs when playing certain chords. Which method should I be using, and if keeping my thumb on the back of the neck, how do I make sure those strings are muted?

Thanks!