question

i noticed that the size of the boxes change with span values but i don t know how the centre of these boxes is determined.

Sim Dimensions is the white boxes I assume you are talking about. You can just use SIM under debug and you get both Sim and Sim Dimensions.

All contact points are based on the Datum Reference Point. Found under weight and balance.

Yes to your question as it does not change the characteristics and is only a reference/location for all the contact points throughout the airplane. So do not change this after all other contact points are set. Always set the Datum first followed by the cg.

Best to have your 3ds modeling program have the center of scene at the center of the fuselage without the tail section included. This way when you set the length of the fuselage it will be from the nose to the start of the tail.

The Datum white boxes are not used. Also do NOT use the orange cylinder box as reference for the diameter of the fuselage. For the fuselage, wing and tail surfaces use the sim from the debug window to see the scale and location using the small green points and ignore the white and orange boxes.

Also it does change in scale from wing length but ignore this as the fuselage also changes. Only the wing length and the datum position is good for viewing using these boxes.

The longitude of the wing is no longer used and you use the Aero Center Lift under Aerodynamics.

flight_model.cfg - [AIRPLANE_GEOMETRY] (flightsimulator.com)