The passport acceptance agent will take your application, photos, checks, proof of citizenship (typically your birth certificate), and send them off to the Passport Office. In a few weeks you will get your passports in the mail along with your birth certificates. They are quite good at ensuring any official documents are returned to you. 6 weeks is a good rule of thumb from start to finish. 4 or 5 weeks is often the case.
Case in point: we sent off for our son's passport last August. For our area, this means it went to New Orleans for processing. Then Katrina hit and I was worried that everything was hosed. My concerns were unfounded. They secured all the applications in New Orleans and moved them to the Charleston office. We got our son's passport and his birth certificate in the mail about 7 weeks after our local circuit court sent them in. (For us, the county circuit court is the passport acceptance agent). I was highly impressed by the Passport Agencys ability to recover from the hurricane. They were one of the few government entities that had their act together.