Well you record a new individual audio track every time you film a shot, so your audio should never be mismatched to the movement of your actor's mouths because for every video clip from every angle there should be the matching corresponding audio clip that you recording with it.
To answer your first question, when you are filming a scene with one camera, the timing and pacing issue to make sure all the shots line up and flow right is mostly done in the editing process.
Other than that you just have to make sure the movement and position of your actors is consistent from take to take. You can sometimes put placemarkers or little X's made out of tape on the floor to make sure your actors make it to the same location on every take.
Also you want to make sure you film more of an action than you intend to include in the final shot. For example lets say you have two shots:
Shot 1) Tracking shot from behind as a character carefully approaches a door and opens it slowly, and steps into the doorway.
Shot 2) Stationary shot from the front, the character stands in the threshold and looks around.
You wouldn't want to start filming Shot 2 with your character already standing in the doorway. You would want to start filming Shot 2 with your character opening the door and then stepping into the threshold. Even though the action of your character opening the door is fully covered in Shot 1, it still gives you some more room to make the cut transition between the two shots with better timing and flow.
Is this the type of thing you were asking about?
"Important dialog is only in Hollywood films" - Kyle Phillip Johnson