When a fleet is selected the ship icon shows a flashing white outline. The ships in this fleet appear in the toolbar display. The first step, using the arrows in the toolbar, is to select the ships you want to command. You select ships for movement or mission orders. 

Normally, all the ships are selected by default.  If you want only a portion of your ships to perform a mission or move, you can control which ships are selected with the arrows in the toolbar next to each ship type. 

When you give movement orders, the ships not contained in your selection remain behind. The toolbar arrows do not permit you to select particular ships of a single category. If you want to make a more specific selection of forces you can use the fleet book.