our diocese has a special program for people in your situation, who have been living together and have children. Some were married civilly and some are common-law, which we still have in Texas. These conferences are exceedingly helpful, especially in resolving the difficulties that have prevented the couple from marrying in the Church. What also happens is that often one or the other has never completed first Communion or Confirmation, they can begin studying for those sacraments as well, and celebrate the sacraments after their marriage. Since children also end up getting baptized or first communion - wow what a powerhouse of grace for these blessed families.
forgot to say the most important thing, pastor or diocesan family life office can help make arrangements with military diocese for chaplain to oversee marriage prep, infant baptism classes etc. for someone on active duty. Please inquire with the person in your parish directly responsible for marriage prep (not the secretary, the pastor or deacon) or contact the Family Life office of your diocese.