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Rocksmith? Why not try some Slayer? To answer your question though.
I'm not sure how the game mechanics work, but in real life, some chords use all the strings, some use fewer. You have to learn them basically. Chords diagrams should indicate which strings are played and which are muted. It comes down to theory of how chords are built up and how the notes on the guitar are located. The advice about JustinGuitar.com is well worth following. Pretty soon your callused, gnarled fingers will endure pain and torment along with the best of them.