for the low E string i use my ring finger, muting the A string below it by gently resting that finger across it. i use myindex finger on the D string, again muting the string below it with my index finger. i use my little finger on the B string, again using the same muting method.
it makes it easier if you tilt/angle your fingers so they lie closer to the strings making muting easy. it is quite a subtle technique, and i'm sure it is the right way to do it.
hope this helps.