Auto focus is a very complex thing because they are many situation in which the auto focusing method could be confused on which to focus. Such example is trying to take a photo of an animal in a cage. The cage is in between the camera and the animal that you wish to focus. I guess Ai AF is a more advance method. Not sure exactly how good it is. 3 points you mean you could choose any 3 of the auto focus square for composing. Usually the focusing square is in the middle, but in this case, it could be either left or right(or middle) which you could choose.
Fill in flash is a detached flash in which you want it to fire from another angle. They are usually the extra flash to produce more lighting from another angle. Slow Sync is using the flash with long exposure. There are 2 types. Front sync flash and rear sync flash. Take a look at this for more details:
You can use the camera's built-in flash or another camera mounted flash as fill-in flash too. Basically this is usually used when your subject is strongly backlit, in which case you expose for the foreground and illuminate the foreground with fill-in flash.