I'm going to "state the obvious" for many, but for the novices (like me to P3D). You can use Plan G (not connected to FSX or P3D) to plan your flight ... adding in waypoints, etc. Make sure to save the "pln" file to Libraries/Documents/Prepar3d V2 Files. You can then go into P3D and "load" the flight plan. Pretty simple.
This also means our flight plans for RTMM can be moved over to P3D without a problem, they are all compatible.