Name them according to their names in tf2_sound_misc_dir.vpk/sound/ui
Everyone knows the default hitsound is named "hitsound.wav", but there are other hitsound files that correspond to the other hitsound options in the menu. Some have one audio file, like the Beep and Space options. Others have several files that play randomly, like Percussion or Note or Electro. I only tried replacing the Space one (sound/ui/hitsound_space.wav) and it worked, but the sound was sped up no matter what sample rate I set it to (tried 44100hz, 22050hz and 11025hz). But it does work, as long as you name the file properly.