Here's the way I do it:
1. Set your view to left view, so that all coordinate data matches what I will tell you. Remember: TS left view gets converted into the front of the ship in FS. Axis switch or something.
2. Make the turret and barrel as seperate objects-this should be obvious. Bring up the model info window (right click the select tool, I think) and change the name of the turret model to "turretxx" (where "xx" is the number of your turret). For the barrel, call it "turretarmxx". Set the turret body location to the point where it is centered on both x and y, and the bottom surface of the turret is on the plane z=0. Place the barrel also directly above the origin, but to the height you want it to be.
3. There should be a button, I don't know where it is in 4.2, that has three arrows: one red, one green, and one blue. Select the turret body and press that button. Then place it at position (0,0,0) so that it aligns with the origin (you can also bring up the sub-tools and select normalize location). Select the turret body again to lock in the axis position. Now do the same for the barrels, but this time set the location to (0,0,z) where z is the height of the pivot point you want the barrels to have. When you convert, Freespace will use the axis of each sub-object to determine point of rotation.
4. Make a local light, move it to the same location as your barrel pivot point, and with the glue as sibling tool, join it to the barrel. Call this group "turretarmxx". Then create another local light, move it to position (0,0,0), select the turret body, and group the new light, the turret body, and the "turretarmxx" group together using the glue as sibling tool. Name this group "turretxx".
You may want to save the group as an object that can be used in the future; it comes in handy. Now you can safely stretch, resize, move, or do whatever you want with the turret and it will maintain its pivot points in game. And a tip: the barrels of two-part turrets always point directly up or down. Don't try doing this differently; it does not work.