Ships must be controlled somehow, be it through a cockpit, bridge or other system, and these systems are termed control systems. On the SSD, this is specified as either Bridge, Aux Control, Emergency or Flag Bridge.
On the ship tables, you will notice that every ship class has a Control rating listing for it. This is the minimum amount of boxes that must be allocated to Bridge, Aux Control and Emergency Control. How this is allocated is up to the player, but as a general rule, Emergency Control is 1 box, and Aux Control is usually around half the size of the Bridge.
A Flag Bridge need not be allocated unless the ship is designed to lead other ships, in which case a Flag is pretty much essential. A Flag is usually upwards of 50% the size of the Bridge.
As a guideline, Colonial Warships tend to have large bridges and small Aux control units, not using emergency control at all. This favours their style of large spacious bridges. Cylons though, have a mix of all three units representing the fact that through their Information Network, the Cylon commander can effectively control the ship from wherever he is within the vessel itself.
As a general rule, the F&E rating should equal, roughly, the value of the bridge and Aux con boxes. Non-warships should lower this rating by around half, while civilian ships shouldn't have one. A minimum for a warship is 2. Ships with a flag bridge may add 1 if they have 3 or less Flag Bridge boxes, while ships with a flag bridge or 4+ boxes may add 2 to the score. Compare with other ships for more specific values.