best to first read the sections on waypoints in Using the Flight Planner, and the sections on VFR Flight and ATC in Flight Simulator - in particular the Flight Following Service feature and IFR Flight and ATC in Flight Simulator in Air Traffic Control in the FS2004 Learning Center
the default flight planner permits for the use of the nearest VORs, NDBs, intersections and airports as waypoints, while user defined or custom way points are only feasible by modifying the flight plan .pln files
and if the IFR plan is filed correctly and/or the flight following service is requested for VFR flights, then the ATC ought to direct appropriately
finally, for patrols with identical origin and destination, as opposed to the typical Direct-GPS, choose instead VOR to VOR or Low Altitude Airways as the Autorouting method when setting up your VFR flight plan - and at your last proximal waypoint prior to heading back to your start location/destination, tune into the ATC to 1) cancel VFR flight following and 2) to request a full stop landing; for IFR flights, best to select a nearby or intemediary 'dummy' waypoint within the proximity of your destination, and upon reaching the said dummy waypoint, cancel your IFR flight plan via ATC, and head back to your origin/destination