From Desert Operations Wiki
When your Units are delivered from the Trade they are safe in the depot. There they cannot be a victim to Espionage and attacks from your enemies. But from the depot the units do not defend your base. Advantage: The units cannot be destroyed. But he fix cost stay the same.
In order to use your units for attacks or for defending your base, you have to place them into one of your three fleets.
For this you go to the military overview in the Command Center. All the way on the bottom under ("Unit Arrangements") you can see which units you have available and where they are located. You can simply move the units to the desired location, for example: "Fleet1" and click on the button "Rearrange Units". If you would like to relocate all the units to the same fleet, you can simply press the button "All Here". It is the same for the depot. You can have the same troops in all of different fleets and depot.