Oh blimey. OK, you see the big VP archives in your main FS2 directory? Those have all the models, maps, missions and tables and stuff. You need a copy of VPView (check the HLP downloads). Use it to open the Root VP, and click Tables on the left-hand menu. You should be able to guess which tables do what from their names. To edit them, you need to extract them to data\tables - use Wordpad or something similar for editing, but be mindful of the limits (ships and weapons must be less than 380KB, with less than 130 entries in your ships table. Other tables have the limits explained within them)
Now, you need to appreciate the way the game searches for files. First, it will check for non-archive files in the data\whatever folders. Then it checks the data folder, then the main FS2 directory. After that, it checks for the file in the VP archives, After that, it lloks for the files on the CD, and then in the archives on the CD. Thus, files in your root FS2 folder will overwrite those in the data folder, etc.
