The Hard point is tied in two places to the UI for the game and to the HPs on the model.
on the model you will have points called Hardpoint1, hardpoint2, etc. these are the actual physical points the weapons when set to them fire from. Hardpoints1-9 are heavy weapons and 10-19 are phaser there is a 21-24 area but they can only be used by certain ships based on coding in the game for that UI.
So...
if the model doesn't physically have that HP on it then they fire from the center of the ship. Also if the UI doesn't support that HP then you can not select it in game it will not show up, for SFC1,2 and OP. Hardpoints can only be done in the modelling program milkshape, and Max. Most programs have this area for placing them/moving them in the Skeleton section of a model.