rotate the modelso you have desired placement of your weapon in view. Then press "locate" button - it's on the top bar of MPE, farest to the right (it has an icon with arrow and black goo on it).
Now, that you pressed it, you can't see the difference but your cursor is a pointer now. Move it to a desired place on the ship's hull and press ONCE. This position will be remembered. Avoid clicking again in the 3D window, or your position will be overwritten.
Now open editing of the weapon you want to add, click "subsystem properties" then find "get position" button and press it. The coordinates remebered by MPE will be pasted in, and weapon should be now exactly where you pointed.
keep in mind that you always can type in coordinates manually or adjust them.
I encourage you to search the forum, I think there was somewhere a detailed tutorial about using MPE
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