I finally found an attorney who was willing to do a free consultation and she was very helpful. She happens to practice Philippines law also so that was helpful for stuff we need to deal with on that end of things (dual citizenship, ect). Anyways here are the answers she gave me specifically regarding the N600:
As far as the information for his biological father goes she said that is not applicable as his name is not on my step sons birth certificate. She agreed with my suggestion to note that in a cover letter. She said enter "n/a" in all the fields for that section.
As far as the date his original passport was issued goes she told me which government agency in the Philippines to contact to obtain that information.
For the section where it asks for evidence of his citizenship she said his mother's naturalization certificate and his birth certificate are all we need. Some people suggested getting his US passport first then uploading that as additional evidence. She said that is not nessasary.
Hope this info helps someone else who has the same questions.