We are happy to share this information with you. 

If you wish to use ATC and FSX Pilot, here is what to do if you are going to use a flight plan.  Create a flight plan using a flight planner and then import it to FSX Pilot.  When the option to also create a standard take off and landing procedure for fixed wing aircraft comes up, hit no.  Do the same when it asks about helicopters.  Save the flight plan, and then load it.  Do not use load and run.  Once at the runway you wish to take off from, make sure autopilot on FSX Pilot is turned on, and then go to the FS Panel and go to Menu and hit run straight take off.  Once airborne, enter the assigned altitude into the altitude box on FSX Pilot, and also check the speed to make sure it is where you want it.  You have to do this quickly in order not to miss ATC instructions.  Once ATC tell you to use own navigation, go to the flight plan menu, and hit run.  There you go, the plane will now fly the flight plan via the waypoints without going through the whole take off procedure.  Same thing when approaching your destination.  Follow ATC instructions, and once you have made the final turn and ATC tells you to contact tower, acknowledge it, and then go over to the FS Panel.  Select the assigned runway from the list of runways at the target airport, and then select which approach type ATC has told you to use.  In other words, if ATC has told you to plan for an ILS approach, use the ILS Auto Land function on the menu on the FS Panel.  If you are doing visual, you can probably use GPS Auto Land or Traffic Pattern auto land if you are going into an uncontrolled airport. 

Thank you, Jordan Gallacher, for figuring that out.