The first thing to remember is that you can only have 3 weapons max (though you can use abilities to add more example the gauss guns and their missile attack ability). Second is that you would need to modify the model/texture of the ships to add the extra weapons (well you could set it for the mid-point of the ship but it would look lame). After that its fairly simple.

Capitals and Carriers need FLAK. The sooner all the strike craft are blown to bits, the better the game runs.

All great suggestions, but what I'm really after is advice on maintaining balance when I add the weapons.

The models are really fine with me as is, I'm pretty much fine with having the weapons just fire out of arbitrary spots on the hull, since I don't have much modeling experience (and what I do have is pretty useless).

Well, since weapons/ability hardpoint are included in the .mesh, you will need to use XSI in all case... but first, you will need to convert the .mesh to a format that XSI can open... to my knowledge, the only plug-in who exist is for 3DS max... everything ( almost ) is possible with sins but nothing is really simple...