Military can be moved from the stationed military box to a ship, and vice versa. To do so you first need to select the ship that you want to assign ship-crew to. Click on the desired ship in the Ships in Orbit list-box. This will display the currently assigned ship-crew of that ship (if any), or empty icons that indicate empty seats inside the ship.
In this case no ship-crew is currently assigned to the ship at all. This is also represented by the red ship-icon in the list-box. A ship will require a minimum amount of crew-men to fly it. This is indicated by the red empty military icons. However, a ship also has additional seats for extra crew-men. These can be used to raise the overall rank of the ship, or just simply for transporting purposes.
There are several methods to assign crew to a ship. One would be to right click on a military in the stationed military box, which would list the menu-item Assign to Ship-Crew. You could select several military (for instance by dragging the mouse over them) and then using the Assign to Ship-Crew command.
The easiest method to (un)man a single ship is by double-clicking on either the red or the gray empty military icon. This will automatically move the highest ranked military over to the selected ship. When double-clicking on the red icon, only the minimum number of crew-men required to fly this ship will be assigned to it. By double-clicking on a gray icon however, the ship will be filled up to its full capacity.
You can dismiss ship-crew the very same way: just double-click on the very same icon that used to be gray, to dismiss the optional ship-crew. Or, double-click on the military icon that used to be red, to dismiss the entire ship-crew. Try it, it’s really convenient!
Later on in the game you will need to manage dozens or even hundreds of ships. In order to ease the handling of so many ships, it is possible to select several ships in the ships in orbit list-box, and right click one of them. In the context-menu navigate to the sub-menu Ship-Crew. In there you will find several options to assign and dismiss ship-crew for all the selected ships with a single click.
Make sure you do have enough military stationed on your planet when assigning crew to multiple ships. The ships will be filled only with military available in the stationed military box.
The rank of the ship-crew does have an impact on the firepower of a ship, hence the same ship with a higher ranked crew will be stronger than a ship piloted by a lower ranked crew. When assigning military to a ship-crew, the average experience for the ship is calculated. The higher the experience of military aboard the ship, the higher the rank for the ship will be.
You can decide to either sufficiently man a ship, or you can add extra crew up to its full capacity. If you add more crew aboard a ship than is required, the rank of the ship climbs as well. The rank of a ship(whether the ship is fully or minimally manned) is calculated by adding up the entire experience of all crew-men, and dividing that by the minimum number of crew that is required to fly this ship. The resulting rank is the rank of the ship, which determines how much its firepower is increased during combat.