Skipping Strings

How does one strum a guitar with X'd out strings (E or A)?

For myself, if I can manage to deaden the A string with an adjacent finger I'll do that, else I just strum the top four strings, as for the E string, I just miss it out as necessary.

I can't tell you how I learnt, it "just happened". Probably not a lot of help for Pete Townsend-style "windmilling", but for a more restrained style it seems to be almost natural ... I do the same thing on a 5-string banjo or a re-entrant ukulele when I don't want the treble emphasised and I've never really thought about it before :confused:
 
I will mute the unwanted strings with the fingers that are doing the fretting. If it is the sixth string, my thumb will sometimes do the muting and sometimes the finger fretting the fifth string.

For a D7 - X5453X, I'll probably use my ring finger to mute the 6th and my index to mute the 1st.
For a D7 - X00212, I'll likely use my thumb (or sometimes fret the 6th string at the 2nd fret with my thumb.)
 
It's more of a click than a plunk. You can hear it if you play that string individually, but when you strum all six strings, it's inaudible.
 
I often fingerpick guitar with my (right-hand) pinky planted by the soundhole and my palm resting just behind or atop the bridge. It's easy for that pinky to slip over to mute top strings, or for my palm to lean down and muffle lower strings. If my right hand isn't in position for such, my (left-hand) pinky or thumb can mute the 1st or 6th strings as needed. But if I'm wearing metal fingerpicks and wailing away (not quite a Pete Townshend) I don't worry about muting strings. More power!
 
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