You give orders while the game is paused to avoid the frantic rush of a real time system.
Once you control a territory, you can decide what type of base you want there: Research, Military, Manufacture or Biomass repulsion. Once the game is underway you can pause the game at any point to update or change your orders and the game will automatically pause when important events occur, so that you may modify your plans accordingly. These attributes are: Strength, Agility, Dexterity, Willpower, Intelligence, and Perception Strategy - You must manage your bases, interceptions, and squads. Territory is equal to power in the game - the more you control, the better your interceptor coverage.