whenever i alternate pick past the D (thats the G, B and E) string, my thumb rubs against the strings. i cant really hear any flaws but i get this feeling it might be wrong. is it wrong or doesnt it matter?
There's nothing flawed about having your thumb resting against the top strings while you play. You've got nothing to worry about. It's actually a good habit to get yourself into. Having the base of your thumb resting on the strings is extremely useful when it comes to muting unwanted noise.