Whoever told you that at NAVPTO obviously does not know anything about immigration law. That is absolutely not true. If he is your son and not your stepson, then he can get a U.S. Passport depending on his age if he was born in the Phillipines, and assuming your are a U.S. Citizen. You will have to petition for a green card for your wife if she doesn't have a U.S. Visa. Having Military orders, PCSing plays no role when it comes to Immigration Law. The only benefit is having deployment orders which you can use to request expedite of the process. Good luck to you!