You use an editor.

Create a pwad that contains modified versions of the
corresponding sprites. There are several ways to do that ; the
one I know is to extract the sprites from the iwad :

 deutex -doom2 /usr/share/games/doom2 -sprites -xtract

With a pixel editor, do the necessary changes in ./sprites/*.
Edit ./wadinfo.txt and remove everything except the parts of the
sprites section you modified. For example, if you touched only
./sprites/bfgga0.ppm, ./wadinfo.txt should look like this :

 [sprites]
 bfgga0 -81 -116

Build the pwad :

 deutex -doom2 /usr/share/games/doom2 -build mywad.wad

There may be other things to take care of, like offsets. Some
stuff might require hacking the exe (Dehacked). I'm not sure, I
never did much of that.