by which you mean emptied? or deleted? or does it matter.
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Deleted. It's useless. Did you move the le version of 000-default back to sites-available (to back it up)?
The only things that should currently be in sites-enabled are:
Don't forget to run these:
sudo a2dissite 000-default.conf
sudo apachectl -k graceful
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Which conf file is that in?
I think you might have gotten ahead of me, which is fine.
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You seem to be of a higher knowledge/experience level compared with many we see here.
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-rw-r--r-- 1 root root 627 Aug 26 00:46 gadgetdailynews.co.conf, if that's what you mean. These things are incredible; they just use plugins to trawl rss feeds and populate themselves with content daily. I guess he runs ads on them, or that's the plan? They get a fair amount of traffic for things built with bots.
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You seem to have things in hand now. 
Just manage the individual port 80 vHost files and let certbot create your port 443 vHost files. Don't be afraid to delete certbot's created files and just have it regenerate them as needed.
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well I have been staring at these webroots for like a couple weeks now, so I'm kinda familiar with them. And now with the limits of multiple vhosts (my original plan had been one big honking server)
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I think you've got a smooth setup going now. With each site having its own two vHost files and individual certificate lineage in certbot, your world should be simple.
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