Does the state have jurisdiction over my children to be able to decide custody?

My ex got an ex parte order. While I was in jail on trump up domestic violence charge against him. He has never legitimated my children. The court order him temporary custody. Here is the thing, my kids and I have never lived there. Only contact we have is visits, but their dad has property their but does not reside at the property. Their dad took them back to our home in another state. I have not been able to see my children for two months. Also I read that if he has not legitimate the kids then legally he should not have them. Should I try to fight this case in the state or ask an attorney to file a motion for dismissal?