Well you don't have to copy your assets, though it does make things easier, and you need to remove them from your steam directory during testing anyway and of course you've got them in a backup folder anyway. My point was that using PackBSP is a bad idea since it is piece of crap, and using auto-scan is a bad idea. We've known for 6 years that auto scan doesn't work right, dunno why people still use it.
ESPECIALLY since doing multiple pack operations on the same bsp to add the assets you missed is a great way to corrupt it.
Anyway my point was that since you've organized your custom assets properly all you have to do is select the folders their in with a manual add operation, and neither PackBSP nor VIDE supports manually adding assets in groups like that.
But what do I know, I mean, it's not like 99% of people have problems with paking and I don't.