or I could drop in and give the lowdown

a lot of the mod programs I will mention, minus Delftship, are in the mod links thread.
a short while ago I found a really neat program that is used by professionals to draft ships. it's called Delftship and I'm not sure if it exports to .obj format
(.obj is the format the 3d models use in SH)
but it is a fun program, and you can use it to get the base idea on how you would like to build a ship from scratch.
but, let's say you want to "kitbash" a 3d model from the game, (The de ruyter ((or however you spell it)) is a good example, it's based on the Graf Spee model) First you download S3D, find your model,
1. if you are looking for a surface ship, it will be in data/sea
2. if you are looking to modify a submarine, it will be...well, in data/submarine
find the .dat file. and use S3D to open it. when you do, on the far left side you will find a list of nodes and other pieces to the puzzle that make the ship. what you are looking for should be almost at the top, and has the ship class name (like NSS_Balao, for example) there, and you should see a little cube icon nearby that says 3D Model. click on that and on the screen to the right you should see the option to import/export. click export and just hit ok for now.
then, download Misfit Model 3d, I use it and everyone "thinks" I'm a 3d modeler

you can use misfit to open up your exported .obj file and edit/modify/destroy/do whatever you like to it. once you learn the program, it's really simple, and if you need any help in that regard just PM me and I will always be glad to help.
I'm guessing that's what you mean by "building ships" but if you want me to explain the 3d model import/export process further, just let me know.