Open up assets1.pk3. Drag-and-drop the effects, shaders and gfx folders into your base folder. That's it.
(If you can't rename it to a .zip, open up your base folder, then open a new My Computer window and go to the Tools > Folder options menu, go to the view tab and make sure Hide extentions for known file types is off (It's stupid to begin with...):
Next, open up your renamed assets1.zip file by double-clicking on it. Now you can copy and paste the effects, shaders and gfx folders from it into your base folder.
When you're done, don't forget to delete your copied assets1.zip, because it's a rather large file.