You might consider the IRC channel if you need hel with the file structure - it's pretty well known, and there're always people idling ion there who can explain the basics In essence though, models are pof files, which can be generated using a proggy called PCS2 from standard geometry formats like .cob and .obj. Textures are preferrably in .dds, but tga will work too (as will, technically, jpeg and 256 colour PCXs, but those are a bit outdated). Ship attributes are defined in .tbl or .tbm files, which you can read/edit in notepad (they're essentially the same files - tbms are modular while tbls are larger is all). The oriinal game files are packaged in VPs, for which you'll need something like Maja or VPView32.
Hmm... writing it all out quickly like that, it seems complex, but it's really fairly intuitive - the tbl files are standard ASCII, the pof files are barely modified geometry (it just adds the stuff the game needs, like firepoints and engineglows)- the extensions are unique but the content really isn't. There's really good documentation for all this on the wiki too.