I applied today for expedited passports.
To answer dandan's question you need for your son the birth certificate, green card and at least one nat. cert. I'll tell you how it worked for me and perhaps it applies to your case.
Took the whole family to the Agnew post office in Santa Clara, CA. Got a knowledgeable acceptance person (I had actually gone a couple of weeks ago to check what I needed). Processed one application at at time. She made photocopy of my wife's naturalization certificate and attached it to my child's application. For my child I needed original birth certificate, copy of naturalization certificate (the acceptance person made the photocopy and certified it (at least she wrote something on the photocopy), and the green card.
Only negative is that she stapled the naturalization certificates. Not a big surprise as it has been mentioned here a few times. I mentioned that to her, but she said she needed to staple and that I would not be happy if the certificate got lost. She got a point
Bottom line: We could process the three passports with two naturalization certificates. If your acceptance person refuses to do this, go to another post office.