Ah, you need to extract it from the .vp first. The extracted file will override the .vp file. See, VP files are a container file, with many files inside them. The files cannot be edited inside the .vp. You need to extract it. Inside the .vp are folders... FS looks for files in the real folders (the ones you can see in Windows Explorer) first; then in looks inside of the .vp. So, if you extract a file from the .vp, and place it in the actual directory, FS will not look at the file in the .vp, but will instead use the one you extracted.
Now, the file you're looking for is ships.tbl, you need to extract it from the .vp It is in the /data/tables directory inside of the .vp, so you need to place it in \FreeSpace2\data\tables, then you can edit the copy that is outside the .vp, and the one inside will not be used.
See?