They're calculated from the model's center for the most part. (Turret firing points are calculated from the base model's center.) If you really want to edit stuff like subsystems, try ModelView32. It's good for most stuff, and good for seeing where stuff you setup in PCS will be on the model. (Example: Edit thruster data in PCS, go to Save, switch to ModelView32, hit Reload make sure the Thruster button is down, and look where your thruster went. Make adjustements as needed till it's right.

) Thrusters, paths, and a few other things are the main stuff you should do in PCS. Subsystems, turrets, and stuff are easier done in ModelView32. At least until Kazan finishes PCS's render view.
