[Treetop64]

Depends on a lot of things, and there is no short answer, but the simplest answer is that for small modifications on an existing model, such as adding pylons or dive brakes, one could start by appropriately editing the values in the sections for drag coefficients, weight, and CoG in the aircraft's flight dynamics file. Depending on the fidelity of the dynamics, the dive brakes could also employ values for aero effectiveness and physical deflection (no matter how slight) at different angles while deploying and when fully deployed, pitch moment while deploying or deployed, and possibly yaw and roll moments for asymmetric deployments, etc.

Then you have the visual side of things with the aircraft model with adding the pylons, and adding the dive brakes and it's animation, possibly with new bones and joints/spindles/etc as well. Usually, the flight dynamics file doesn't care what the visual model looks like. The aircraft will fly according to how the data is written in it's configuration and flight dynamics file, regardless of how the visual model appears, so it's important that the visual model is deliberately "coordinated" with the dynamics by the author.

As for new wings and powerplants, things can get more complicated. A redesigned wing will usually have a new NACA profile (basically, the proportions and contours of a wing at different cross-sections along it's width), different wing area, and numerous coefficients defining it's behavior at different speeds and angles of attack, among other things. The fidelity of the engine modelling depends greatly on how sophisticated the host application is. If the new engine has a new propeller, then new prop efficiency data must be entered (efficiency curves, advance ratio, power coefficients, etc...).

It can be much more work involved than one might initially assume. You'll also need to know and use proper maths/formulas.

Modifying a real-world aircraft will usually alters it's CoG, flight, and stall characteristics, and all that must be accounted for, figured, and entered into a simulated aircraft's dynamics file.