Check the file structures in the various .vps... Especially the vanilla FS .vps, if you have them. The .vp files are generally just stuff inside the /data folder stuffed in to a package for easy transfer/storage. The game however will always check the game /data directory first, and will use anything it finds in there. So for example, if you have the aurora.pof in /data/models directory, the game will use that one instead of the aurora.pof found in TBP .vp files.
Same goes for all other files. Tables, music, anims, textures, everything.
As for the folder names... The TBP .vp files should have the file structures intact (I think)... So you can check them which file goes in to which directory. Since you're modelling, you need to put the .pof in /data/models, textures in /data/maps. And tables go in to /data/tables.