Help with flightplanner waypoints

Hi guysIve just started to get to grips with the flight planner within fs2002 and have used it to successfully fly autopilot routes within europe. However, this may be a stupid question but it stuck me that, whilst flying within europe, i can enter waypoints such as vor's into the flight planner for the autopilot to follow. However, what method is used when flying over large expanses of water such as the atlantic or pacific? Also, when entering waypoints, is there a "protocol" to follow when selecting the actual waypoints to enter ? Thanks for any helpGary