This is obviously pretty opinion based as you can see above, but I do it a different way than everyone else it seems. I like keeping my tf/custom folder clean for HUDs, hitsounds, my medigun and texture improvement pack vpk etc. Just custom stuff used by the actual game, not Hammer. I keep the root tf folder clean as well since some files are kept loose in there when you install the game. I don't want to contaminate that because, again, it becomes difficult to see what's custom and what's not.
What I have done is made another tf folder, called tf_dev. I have it follow the same folder heirarchy as tf, but everything in there is custom and doesn't get referenced by the game. This is also helpful when you have custom content and you're checking to see if you packed correctly. When you put your custom content in the tf or tf/custom folders, the game will see it and pull it up even if your map didn't actually get it packed. If it's in tf_dev, you can setup Hammer to see it but the game won't.
If you're interested in doing it like this, just let me know and I can show you how it works.