Depending on the state you reside in, I know VA you can. You should be able to fileseparately for child support and custody. Then later have the provisions added to your final divorce decree. If you are living separately and have reason to believe that custody will become an issue, you are risking a lot by not going to the courthouse and simply attempting to file for it. If you don’t have an attorney to advise you, get on line and start doing research in your states on line law library. Sometimes, in nasty situations, people are unaware that a divorce can take a long time, however custody is usually quickly resolved and without it, either parent can take off with the child wherever they choose. Good luck.