It was long ago when I installed the Half Life Quakux mod but I do remember some things I did to make it work (with help from fuzzi23). Here are the files I had in my Quakux folder:
Inside the Quakux
folder, you should have the ID1
folder, the valve
folder, the Quakux file
, and HalfLife.dge
Inside the ID1 folder you should have these files: config.cfg, Pak0.pak, PAK1.PAK.
Inside the valve folder you should have these files: (gfx folder, MAPS folder, MODELS folder, PROGS folder, SOUND folder, SPRITES folder, autoexec.cfg, CONFIG.CFG, dingoo.cfg, gfx.wad, progs.dat, quake.rc)
Make sure you do not have
the Pak0.pak, or PAK1.PAK files in the valve folder or the game will not launch.
Hope this helps!