I'm new to the guitar and have been going through Guitar Fundamentals for the last two weeks with Anders. Today I started going through Lisa's Fundamentals as well, but am not as far through. With that said, it's possible my question is covered in later courses. But thus far, all of the instructions about playing chords that don't include all of the notes teach me to just avoid strumming those notes. The most common examples are the C and D chord. 

Recently I was talking to my nephew who has been playing for a long time, and he told me that when I play those chords, I should be muting the Low E with my thumb. He said to make sure I practice that now in order to develop the habit. When I asked about just skipping those notes when strumming, he said no experienced guitar players do that -- they all Mute with their thumb. It's also worth mentioning that at that point I was actually positioning my middle finger slightly higher on the A string so that it was muting the Low E. He said I definitely should not do that because I should focus on good finger position and not develop bad habits.

So here's my question. What should I be doing??? It seems like it would be really difficult to avoid strumming the Low E and/or A while also keeping a good rhythm, but I also understand that right now a lot of things seem hard. Is that actually a skill I should work on perfecting, or should I be making it "easier" on myself and muting with my thumb?