The best way to begin with re-texturing something is to check the original resources and modify them.
So use the ArchiveTool or ArcExplorer to get texture (*.tex file) out of Creatures.arc, TerrainTextures.arc or any Scenery.arc. View it with the TextureViewer and export it and change it in your painting program. Save your changed version as TGA, because JPG didn't work during my tests.
Paint your texture
Use your favorite painting tool and modify the texture as you wish. Save it afterwards as PSD or TGA (32bit with alpha).
You can use alpha channels for transparencies. But it works only with special meshes such as any ghost mesh. It seems there is some info stored within the mesh that is needed to create a real alpha texture
Importing and Linking
Create Auto Asset (use the texture option, DXT5 is the most common). For alpha textures use also one of the alpha setting.
After your tex file is created, build it and you can use it as texture parameter in your desired dbr file.
When you auto-create the source file you have to also create a dbr file. Go into art manager and create a new directory. While inside the newly created directory, create another record and choose terraintype.tpl for the template (inside database/templates/). Open the .dbr record and go to the "Textures and Bumpmaps" plane. Change the dir of Texturefilename to your custom-created .tex file. Rebuild and test it out.