If you want a simplistic overview of the FS data structure: (there's probably stuff in here you already know, but I've put it in just in case.

)
It all centres around the tables. The most important ones are the ships.tbl and weapons.tbl.
In terms of how new ships are handled - the ship will have an entry in the ships.tbl which will follows a rough layout (you can find all the information on the layout in the wiki
here. It looks very scary, but really it's piss easy.

Typically, people just copy & paste an existing table entry of a similar ship and then change the bits they need to. After you've copied one, all you need to change to actually get a new model game ready is:
$Name: UniqueShipNameHere
$POF file: FilenameHere.pof
(The tables are just text files BTW. They need no special tools to edit.)
Aside from the table entry, a new ship will consist of a model file (.POF type, and stored in data/models) and whatever textures it needs (.DDS type, stored in data/maps).
The POF file contains a lot of the ships raw data, such as the mesh, textures, UVs, subobjects, shields, LODs and debris, as well as a lot of other stuff such as subsystems, dockpoints, attack paths, firepoints, turrets etc. To create POF files you use the Pof Constructor Suite 2 (PCS2) to convert a properly set up .COB or .SCN file. Since PCS2 allows you to edit the subobject hierarchy now, you don't have to worry about setting it up in the cob or scn. The main tutorials on the actual conversion I'd recommend are Bobboau's PCS1 reference guide (the same stuff still applies to PCS2, it just has a better interface) here:
http://freespace.volitionwatch.com/blackwater/fstut/fstut_index01.htm and Karajorma's turretting tutorial (mainly focusses on hierarchy, and does so in the horribly buggy truespace 3.2, but it might help anyway) here:
http://homepage.ntlworld.com/karajorma/FAQ/shipmods.htmlOnce you've done all that and have your new ship modelled, mapped, poffed and tabled up ready to go, you get it in-game by placing it in a mission (assuming you don't just want to release it at that stage). The missions are created in FRED 2 - which comes with an excellent tutorial in the help file.
And that's about it. There is of course a LOT more detail to every aspect I've covered here, but that's the basic gist of FS modding.

Finally, a couple of notes:
1) The collision mesh used in game is just the visible model - there's no need to make a separate optimised mesh for such purposes.
2) VP packages are just container files - in them they contain the same data folder structure as in the main FS install path.
3) Use TBMs (modular tables) if you want to add individual ships. TBMS get appended to the main table, whereas TBL files overwrite each other. You can read up on TBMs
here, but the main things about them is that their filename is "WhateverYouWant-shp.tbm". The -shp tells the game which table it should be appended to.
As for their contents, it's just:
#Ship Classes
< ship data as it would appear in the ships.tbl>
#End