FSX and FSXPilot flightplans are different. In FSX, a flightplan is just a selection of waypoints to be loaded into the simulator. 

In FSXPilot, a flightplan is a complex program for actually flying your aircraft from A to B taking into account: 

  • switching on nav and landing lights
  • takeoff routine
  • setting departure and destination display
  • operation of flaps
  • operation of gear
  • following the waypoints
  • ILS or GPS autolanding
  • brakes and reverse thrust
  • if you want: taxi procedures

To create a FSXPilot flightplan, you can actually import an FSX flightplan into FSXPilot. This manual describes how. 

Let us assume you want to fly from Munich to Venice with an ATR aircraft. The first step you have to do is startup FSX, load your aircraft and position the aircraft on the active runway in Munich (EDDM).  Please create your FSX flightplan and save the flightplan to your harddisk. Please select the flightplanner in FSX, use "IFR" and "high altitude waypoints". Save the plan. In my case, FSX suggests a flighplan name 'IFR Munich to Tessera.PLN'. Use that name. 

Then, start FSXPilot and select "Import flightplan" from the AP main panel's menu. In the file selector box select 'IFR Munich to Tessera.PLN' you have created previously. After the import, answer the question wether FSXPilot should add takeoff and landing routines for fixed wing aircraft with "Yes".Save the new FSXPilot "flightplan" to disk. FSXPilot suggests 'EDDM_LIPZ.txt' as a file name. Use that name. 

You can open and edit the FSXPilot flightplan  'EDDM_LIPZ.txt' with any conventional text editor. This is what you get: 

 

// -----------------------------------------------------------
// Flightplan for FSX
// for use with FSXPilot
// 
// FSXPilot (c) 2005-2012 by Scientific Networks Munich 
// -----------------------------------------------------------
// add your comment here 
// and here
//
//
set origin EDDM
set destination LIPZ
set speedunits knots
set distanceunits miles
set apcontrol plane
set userinput on
autorudder on
run takeoff
set alt 27000.0
waypoint 27000.0  300.0 EUR  47.73499167  11.24940278
waypoint 27000.0  300.0 OBAGA  47.59861111  11.25000000
waypoint 27000.0  300.0 NORTO  47.26635278  11.25182222
waypoint 27000.0  300.0 MATAR  46.97493889  11.25330556
waypoint 27000.0  300.0 BZO  46.46363889  11.32188889
waypoint 27000.0  300.0 ALESE  46.27499722  11.40388889
waypoint 27000.0  300.0 VIC  45.63730556  11.67635278
find bestrunway LIPZ
select approachentry
flaps 1.
wait distin 2.
select ilsentry
wait distin 2.
select bestrunway
set ils
stop aph
stop apv
end

Feel free to make changes. For example: If you use 

set userinput on

the plane will ignore altitude and speed settings in the flightplan and rather use the altitude and speed settings of the pilot, but still  follow the waypoints. 

Change to 

set userinput off

for a fully automatic flight with cruising altitude and airspeed defitions. 

 

In the line 

waypoint 27000.0  300.0 EUR  47.73499167  11.24940278

change '27000' to a new value like '29000' for a different cruising altitude, or change 300. to 250, for a more realistic ATR airspeed.   Additionally, you might want  to fly a short GPS landing, which looks a bit more realistic, at the destination instead of an ILS landing. 

So with one ore two other tweaks our final flightplan would look like this: 

// -----------------------------------------------------------
// Flightplan for FSX
// for use with FSXPilot
// 
// FSXPilot (c) 2005-2012 by Scientific Networks Munich 
// -----------------------------------------------------------
// add your comment here 
// and here
//
//
set origin EDDM
set destination LIPZ
set speedunits knots
set distanceunits miles
set apcontrol plane
set userinput off
autorudder on
run takeoff
set alt 15000.0
waypoint 15000.0  250.0 EUR  47.73499167  11.24940278
waypoint 20000.0  250.0 OBAGA  47.59861111  11.25000000
waypoint 25000.0  250.0 NORTO  47.26635278  11.25182222
waypoint 25000.0  250.0 MATAR  46.97493889  11.25330556
waypoint 25000.0  250.0 BZO  46.46363889  11.32188889
waypoint 20000.0  240.0 ALESE  46.27499722  11.40388889
waypoint 10000.0  200.0 VIC  45.63730556  11.67635278
fly short autolanding LIPZ
end

Save the changes in your text editor.

Finally, "load" your FSXPilot flightplan via the flightplan menu and select "run flightplan" from the menu. 
FSXPilot should now fly your ATR plane safely to Venice from takeoff to autolanding.

Have a nice flight across the alpes.  

 PS: 

The way back to Munich (ATR turboprop, with short landing on runway 26L)  is for example:

// -----------------------------------------------------------
// Flightplan for FSX
// for use with FSXPilot
// 
// FSXPilot (c) 2005-2012 by Scientific Networks Munich 
// -----------------------------------------------------------
// add your comment here 
// and here
//
//
set origin LIPZ
set destination EDDM
set speedunits knots
set distanceunits miles
set apcontrol plane
set userinput off
autorudder on
run takeoff
set alt 15000.0
waypoint 15000.0  250.0 VIC  45.63730556  11.67635278
waypoint 25000.0  250.0 LIZUM  47.11507222  11.75603611
waypoint 15000.0  230.0 TULSI  47.70160556  11.78875833
waypoint 10000.0  230.0 MANAL  47.89935556  11.79995556
fly short autolanding EDDM 26L
end