Well, if you know how to edit tga files (and their alpha channel) and you also know how to extract tex files with gp4master, i think you know all you nned to edit files.
The way to do it is the following one:
1 - Extract wad file in a folder with Gp4master Wad workshop
2 - Browse tex files in the just created folder and select the one you want to edit with Tex workshop
3 - Choose extract selected file with tex workshop and save the corresponding tga file somewhere on your hard drive
4 - Edit the TGA file with some editor (PSP, Photoshop...)
5 - Open again your tex file in GP4Master
6 - Choose Replace file in GP4Master's tex workshop and choose the downsample button to make low detail textures (or import them in separate TGAs)
7 - In the wad workshop, choose Make wad from a dir and put the path of the directory where you extract the wad in 1
8 - Found where has been create the wad you just created (in the last folder you open with GP4Master generally) and copy/ write on top of the original wad file in your GP4 dir
9 - Verify you did a good work, trying GP4 again
10 - Have a good day