Well then, u need MPE, if you haven't got it already, then download BC SDK.
first thing u need to do is opening model, then u will be asked to load hardpoint load it then look at the rightside bar, there will be a tree of model nodes (similiar to block list in Nifskope) u need to click on 'Scene Root' in order to see all the hardpoints on left side bar.
Now you can modify everything about every hardpoint.
usually for realligning you'll need only 'locate tool' (especially usefull for most of the point-based hardpoints like torpedo launcher or ship subsystem, doesn't work too well with phasers) you can also hit edit and go to position tab and there you'll see XYZ coordinates, usefull for manual reallignment.
that should be all u need for now ;)