This is some of the easiest things that can be done on S3D

.
Once you have the .dat opened in S3D, right click on the main node (the one with the ship name) and
Append new child chunk-->
Nodes (type: 4)-->
Node (type 4/100).
This will add a new node at the end of the list (you may have to scroll down to see it). In this new node you have to add a new label: right-click again on top of it and
Append new child chunk-->
Label (Type: 8/0).
Once you have the label, you need to give it a proper name, which should be something like this:
cfg#X01_NCV_Kaiyo (NCV_Kaiyo or whatever the name of the ship is).
Now you have the node created, but you have to put it in the right place. In
Node positioning you can move the node in the 3 directions (x,y,and z). Take into account that 10 real life meters are 1 unit in SH world. The model preview is very handy for this. Just remember to turn on the
Toggle axes icon button and you will have a visual reference on the model.
Now you have to repeat the process for every plane you want to add, using X02, X03 and so on nodes. A bit cumbersome at the beginning, but when you get used to it you will do it quite fast (when you get familiar with the S3D you could copy and paste the first node, but you would have to do a few more things, like changing IDs and Parent IDs).
Hope this helps you.