glue

Ok... I am a total novice when it comes to this. I am planning on starting my first project this weekend but I keep seeing glue being mentioned. I just assumed that the glue was applied into the screw hole prior to the screw being placed. Then I was reading Ana's start up info and it said-"Insert the screw into the predrilled hole, apple glue, and line up the two boards to join. Don't worry about getting the entire joint precise, you can rotate the board after you get the first screw in. Screw it together" So...I'm not sure what that means! Does the glue go into the screw hole or between the two pieces of wood to be joined?
Thanks for any info, I wanna start out the right way!