I am active duty military who is filing for a divorce from a civilian spouse who resides in brooklyn ny. We have two children and both agree to split

An attorney can file an uncontested divorce action on your behalf, and the laws are the same whether or not you are in the military.  First a separation agreement needs to be negotiated that takes into account any legally required maintenance and child support, depending on the ages of your children. A good agreement will be detailed and will resolve the distribution of all of your joint assets, pension, and real property, and address all aspects of your childrens' lives in which decisions will need to be made, such as education, religion, activities and medical insurance, and leave no loose ends.  The separation agreement will become your divorce agreement when the papers are filed and the judge signs the decree.