-Your son is the applicant, so he needs to sign the Part 5. But because he is a child under 14, you can sign his name (not your name) for him. Just like this format"your kid's name/by guardian your name"
I plan to re his I-539, but his I-94 will be expired after sept. 15, 2009. Can he tays here if the application is still pending?
-He has no problem to stay in U.S. as long as he files the Form I-539 before Sept. 15. So, not need to worry.