That's all a part of puberty! I'm really skinny too. The best thing is to learn how to lift weights, I was lucky because my school has a weightraining class. You should also exercise! But don't worry about it too much, you're still 13 and you've got a HUGE way to go...1 guy I know (adult) grew 8 inches (height) in 1 year, and you've got about 7 or so years to go until puberty is over.
Your body will fill out over the years (chest gets bigger) and your body will produce more testosterone so you can build more muscle. I'd say you should just find a sport you like and work on that to get the athletic thing down, and don't ever skip out on meals because that makes you bigger!