Another quick question.. when adding superstructures to the vessels is there a way to avoid them being superimposed on the secondary guns etc they were automatically generated?
I am not aware of any way to change the precedence of features in the ship profile image using the in-game editor.
If your superstructure is covering up the guns, you can add the guns back in by clicking on one of the [...] buttons below the selection arrows, which will bring up a file menu that by default is open to the ship set you are using. If you type Turret into the file name box (which by default contains something like Mast*, Superstructure*, Deck*, or Accessories* depending on which [...] button you pressed), you should be able to find the image files for the turrets. If I am not mistaken, TurretSm* are 5" or 6" turrets, TurretMed* are 7-10" turrets, and TurretHvy* are 11" and heavier turrets; 4" and lighter guns usually are not automatically generated on the ship profile image but can be added manually if desired.
If your guns are popping in front of your superstructure in the rare case where you might not want them to, then the only way in which I know to fix that is to open the ship profile image file in an image editor after you save the image that the in-game editor generates and edit the image so that the (parts of the) guns which you do not want to be visible are covered by superstructure or other pieces.
A little something that I made for my Confederate AAR but never ended up using. Furor at Dawn, made using CCIP's ship parts set and several hours in Paint, Paint 3D and Paint.net. Hopefully all of the other ship pictures that I plan on using end up this good.
“It is our turn now. So long. The captain and crew of SS Beaverford”
Final message transmitted from the cargo liner SS Beaverford before turning to engage panzarschiffe Admiral Scheer. Her sacrifice, sadly forgotten, saved the remaining ships of convoy HX 84.