In terms of flight planning for PF3, you should generally include in your PF3 flight plan only waypoints you are certain you will cross. Anything that is runway-specific should probably not be included, as you don't know which runway will be active at the time. SID or STAR waypoints that are common to all runways can be included. You generally get the best results if the last PF3 waypoint is about 25-30 miles out, so if you choose to add a SID or STAR using your flight planner you may need to manually remove from the pln file any waypoints that are runway-specific or close to the airport.
The other alternative, seems to be just to forget Sids and Stars and ask for vectors for everything, which doesn't seem to be that realistic.
Standard vectoring is not going to work well in all cases. Terrain and restricted airspace are some typical issues. In these cases you are going to want to consult the charts and fly the departure or approach procedures at pilot’s discretion. PF3 is not going to assign a GPS or VOR DME or DME arc approach. Those choices are up to you and are flown at pilot's discretion.