If you've made a custom wad, put it in your mod directory. For CounterStrike, put it in cstrike, for singleplayer Half-Life or Half-Life Deathmatch, put it in valve, for Day of Defeat, put it in dod, etc. Don't put the wad anywhere else, the game/mod will only look in its own mod folder.
Make sure you wadinclude your custom wad when you release your map to the public.
If you wadinclude from the beginning, it doesn't matter where you've placed the wad file, as HL will read the custom textures from within the compiled bsp file. Hope that makes sence.