You can file for divorce in the same manner as if your spouse is not in prison, as long as you can make sure that the summons is served to him personally through the prison authorities and you have a valid proof of that. Getting full custody of your children will be up to the court to decide, taking into consideration the children’s best interest. However, it will be very helpful if you will be able to convince the court that it is your children’s best interest to stay with you. Work with an attorney who is an expert in family law so that they could help you through the whole process.