Finally! I made a working multi-part turret!!!
Here is what I did.
Start off with at least 3 objects for a ship with one or more multi-part turrets:
Hull
Turret base object
Turret barrel object. (Can look like multiple seperate barrels as many

turrets do, but will rotate as one object.)
Part 1, Rotation and subsystem location:
Arrange the parts the way you want the turret to look. Now, you should make sure that the turret parts will rotate right. Select the base and hit the axis button. Somewhere a little (or big) 3D axis thing should appear and the turret base should go orange. Move the axis to where you want the turret part's pivot point to be. Repeat for the barrel object and for any other object sets if you have more turrets.
The rotational center is, I think, used to determine where the subsystem is shown to be in game. Putting it off center can cause really odd stuff. (Imagine unattached turret parts orbiting the ship...) You might want to check the rotational center of the hull object and any other subobjects too. Now on to the familliar stuff.
Part 2, The turret objects:
Add a local light and glue it as a sibling to the barrel. (Child might work too.) The light's only purpose is so you can have multiple turrets and it shouldn't matter where it is. Glue the barrel to the base as a child object. Repeat part 2 (and if you didn't do it before part 1) for any other turrets. I wouldn't worry about naming this stuff now, you can do that in PCS/ModelView32 and if using TS1 it won't name them right anyways.
Part 3, Putting the puzzle pieces together:
Glue each combined turret to the other turrets as a sibling. (Select a combined turret object, select Glue as Sibling, then click the other combined turret objects.)
Glue the multi-turret object to the hull object and finish up anything else you want to do in TS1. (Like texturing.)
Part 4, Please Convert my Scene (PCS) time:

Save your scene file and pop up PCS. It's conversion time. Set the Options->Scaling Factor to whatever you want. The bigger it is the bigger the ship. Go to the Cob to POF convert item and in the open dialog change the "Files of Type:" drop down list box to Scene files instead of COB files. (If you want to do it by COB instead of scene you can. I use scenes unless it's a 1 object model I'm Cob2FS2ing 'cause my last used scene will auto-load in TS1 next time I run it.

) Navagate to your model file and open it. Before you save it and switch to ModelView32, which I think is better for doing turrets and stuff right now, you might want to fix any mangled texture names. (TS1 doesn't do long file names.

)
Part 5, The nitty gritty:
Save and switch to ModelView32. (You could minimize PCS for now so you can work on thrusters and path stuff without having to rerun it.) Go into Edit mode and name your subobjects. Then test the rotation axis for the turret parts until you have them set right. (If one of your submodels starts orbiting you'll have to go back to TS1 and fix it's axis location.)
If everything worked right then it's time to make the actual turrets. For multi-part turrets select the turret base submodel and give it something like the following in it's properties:
$special=subsystem
$name=Gun Turret (or Missile Turret or maybe other stuff. Not sure it matters.)
$fov=180 (The range in degrees which the turret will target. If outside this range the turret won't fire.)
Go into the Turrets section and make the turret itself. For multi-part turrets the Associated Submodel is the base and the Rotational Submodel is the barrel. A turret with more then one firing point but only one weapon may still use more then one firing point. Haven't experimented with multiple firing points and multiple weapons yet.
6, The home stretch:
Do anything else the model needs, and if you go to do stuff in PCS and didn't close it, remember to save in ModelView and reopen in PCS.

Then make the table file and try it in the game.
Tips and tricks:
The name of the turret base submodel is the name of the turret as used in the table file.
For single part turrets, the procedure is almost the same except you don't have to worry about rotation and have to set both associated and rotational submodels to the same thing.
Turrets on the sides of ships doesn't work. Or so I've been told. I'll have to play with it a while before I'll be sure it won't work. :>
I've been told that strange things can happen when your normals aren't pointing straight up. Another thing I'll play around with.

Boy that was big.