First off I strongly suggest you take the courses in FS2002 that will help you alot do not worry about the check rides as you have to perform flawlessly in order to pass them.
But all you have to do is to open the flight planner and select your starting point and posistion make sure you select a gate or a general avaition spot for your starting point otherwise by default you will wind up on the active runway. Then select your landing or destination
select IFR or VFR be warned if you select vfr and fly with real world weather you will not be able to land if your destination airpor is IFR
Then just select which type of route you want low level altitudes,highlevel altitudes direct or VOR TO VOR. It will then plot a course for you which you can edit if you like to make your flight go to specific waypoints or points of interest along the way.
Once that is done select the plane you wish to fly make sure your GPS/NAV switch is pointing toward GPS. This will allow you aircraft to follow your flight plan exactly as you plotted it. Once airborn you switch on the auto pilot and use the heading switch to maintain runway heading till ATC tells you to turn to intercept your flight path once you have intercepted your flight plan just click on the NAV switch and set your altitude as required by ATC and that is it 8)