In an agreement you can put things any way you need them stated. You can state that you have joint physical and legal custody. Some parents have equal time but that may not be an option for you so you would put into the papers that when you are deployed you will pay her $X amount and that when you are home neither will pay. If you are going to draw up the agreement this way you need to be very specific about what you are covering for the children. School supplies, medical/dental, clothing and shoes. Who will pick the child up, who will drop the child off, who will pay for child care and insurance…trust me that these “little things” can turn into a big arguement. If you and she are able to discuss things as they come up then it’s normal for the parents to change schedules and things in the agreement as needed. Things change, children grow up and their needs change, schedules change. It’s easier and cheaper to use an agreement as a basis for just raising your children together separately than to go through the courts. It’s a good idea to have a consultation with an attorney to make sure that your agreement covers all your rights. You should also put into the agreement about equitable distribution so that that is covered. You are both entitled to 1/2 the marital assets and responsible for 1/2 the marital debt. But you can agree to an unequal distribution. Have the agreement signed and notarized.
If you want to take this through the state then one of you will pay the other and there can be no disruption of payments. Whichever makes more money will pay the other according to the guidelines on the home site (CS calculator). Child support is then based on the income of both parents, the number of overnights with each parent, insurance and child care costs. I think this would be the only need to designate one of you as custodial parent.
I assume from reading this post that you are going to use the last 11 months as your separation? I must tell you that you must put into the agreement the date of separation. You must be separated for one year and one day prior to filing for absolute divoce.