SAS is primarily a naval game, and your main power is projected through your ships (and the aircraft they may carry). Where you deploy them and the orders they have are the most crucial elements in winning the game.
Ships are organised into fleets, and each fleet is given a mission - a purpose if you like - that is the rationale for the type and number of ships in the fleet, where the fleet is sent and what its rules of engagement are. There are over a dozen types of mission, including reconnaissance, patrol, bombardment, convoy, ready reaction, and so on. See the overview of missions for more information.
SAS's very flexible command and control interface makes the task of creating missions as simple or as complex as you want. You have a very able, computerised 2-I-C who is there to help with any aspect that you don't want to handle.
Follow these links to learn all you need to know about forming and deploying fleets.
The links are arranged in order from the simplest to the most complex option.
Option 1 - this is the simplest - just let your 2IC handle everything. He creates all the missions by assigning the most suitable ships, calculating fleet movement orders and setting rules of engagement.
Option 2 - this is the same as option 1, but, after reviewing in the Mission List what the 2IC has done, you can cancel any or all of the missions, returning the ships back to the available pool.
Option 3 - this is almost as easy as the above - while still letting your 2IC make the decisions you can change any of the default settings he relies on, such as the list of approved mission types, and their priority for obtaining the necessary shipping.
Option 4 - this is one step more detailed again. Your 2IC still does the detailed planning but you exercise more control by vaying certain parameters for selected mission types. The most important parameter is setting your own objective hexes (instead of leaving this decision to your 2IC).
Option 5 - here you can elect to edit the actual missions your 2IC creates, after he has created them. For any mission, you can swap ships in or out and change the fleet movemement orders or the rules of engagement.
Option 6 - lastly, you can use the same knowledge you exercised in option 5 to create your own missions from scratch. You can do this for all missions, or just for the ones your most care about, leaving your 2IC to handle the rest. Examples where this could be useful are minelaying and convoying: setting these missions up can be a little tedious and they may not be your most important priority. So, you can create your own "sexy" missions, such as offensive patrol, bombardment or close blockade, while leaving minelaying and convoys to your 2IC. However, if you are an experienced player you may want to manually create all missions without any reliance on your 2IC. This is the most satisfying and potentially the most beneficial option (if you trust your planning above your 2IC's abilities!). But it is also compex and more time-consuming and is best tried only after you have mastered all previous options.