The turret stuff stored in the mission files shouldn't affect anything.
To have a working multipart turret, as a general guide you need to:
1) Have the barrels (arms) as child objects of the rotating base object, and have the base object a child of the main hull.
2) Also make sure that the centres of rotation of each object are in the appropriate places or the bits will rotate all over the place)
3) Make sure the arms on all turrets are pointing directly away from the hull beneath. This usually means straight up or down for regular top/bottom turrets.
4) In PCS2, the subobject properties for the base subobject are set as follows:
Movement Type: Rotate
Axis: Y Axis (This is the up-down axis and is used for turrets on the top or bottom of your ship. You need to use fvec and uvec for anything else)
Properties:
$special=subsystem
$fov=180 (Imagine a targetting cone with the point attached to the turret base, and the rest of the cone straight above or below it. The FOV is the angle of the pointy end of that cone.)
$name=main turret (This doesn't actually have an effect, but is probably still nessecary. Never could be bothered to test.

)
5) In the Turrets section of PCS2, add (if it's not there already) a turret with:
'Parent' set to your turrets rotating base subobject
'Physical' set to your turrets barrels subobject
'Normal' set to point in the same direction the arms are pointing, ie. straight away from the hull below.
Then add as many firepoints as you have barrels with the limit being 3 max and stick them where you want the shots to emerge.
6) In the table entry for the ship, make reference to the turret somewhere in the subsystem section at the bottom. The format is:
$Subsystem: <name>, <percent of main hull strength subsystem has>, <time taken for turret to do full 360° rotation>
$Default PBanks: ( "<weapon1>" "<weapon2>" )
So for example:
$Subsystem: turret01,0.833,1.0
$Default PBanks: ( "Terran Huge Turret" )
There are a few other specialised options you can find in the wiki.
