How do I comment on a Khan Academy project?

You can't comment for three days after creating your account. You also need 5,000 energy points and a confirmed email. After that, there is three comment tabs (Help requests, questions, tips and thanks.) If you have questions about the code and how it works, the question tab is for you. If you just want to comment on how awesome the program is, and give feedback, leave a comment in the tips and thanks. 

Hope this helps!