The children (if they exist) should be included in the whole process as necessary. They need to be part of the changing of the guard ceremony so that they know and understand what is happening between the father and mother. They need to know what their new responsibilities will be, if any. They need to know that while Dad is gone, Mom is in charge. They need to know and understand any arranged plans for the elders or deacons to be involved in the life of the family (if any).
Feel free to adjust anything you see here so that it will help your family to serve God and one another. The duration of the trip should affect the preparation. A shorter trip (for example, a weekend) will involve less preparation for handling responsibilities than a longer trip (several months). If this is the case, feel free to modify what happens during the ceremony. No matter how short the trip is, there should be some acknowledgement that the husband is going away and then another when he returns. The entire family should officially acknowledge this.
This changing of the guard ceremony idea will not solve all the problems frequent and/or lengthy separations can cause in a family. However, official relinquishing of duties and an official reacquisition of those responsibilities should go a long way in making sure communication between the husband and wife is maintained. It helps keep the Navy running smoothly, and it should help the family run smoothly as well.