For most graphical changes
you only need to:
find the relevant texture and/or .shader files from data-1.1.0.pk3
edit textures and/or shaders (shader manual here
recreate the folder structure found inside data-1.1.0.pk3 (only folders you took files from)
put the changed files in the same subfolders and compress those to z-mymod.zip, then rename to z-mymod.pk3
weapons and other gameplay changes you need to modify source code and compile your own game.qvm and cgame.qvm files and put those in the vm folder inside the .pk3.
However, considering your English does not seem very good, you may want to try to ask questions/get instructions in your native language.