tehLulz, download Wally 1.55b ... this will let you import textures from wherever you have them, and export to the BSP directory.
If you have a folder in your pball/textures/, for example c:/games/paintball2/pball/textures/xxx, and that texture contains your custom textures, then you'll have to have a matching folder named 'xxx' in your /textures/ folder in BSP, and you'll have to save the .WALs you export from Wally, in to that folder.
Also, you'll need to attach the palette in Wally, the palette is found in the /paintball2/ folder, I believe.