Today I start setting up a new web server for our small, non-profit. Because none of us are sys admins, we're be doing basically what the previous person did, when he set it up on the old server years ago. We have public facing website for our non-profit, what I like to call "brochureware". It describes who we are, where we're located, etc. The previous guy placed this all in wwwroot. Not a folder within wwwroot, just wwwroot. I've always felt that was probably wrong, but I didn't know any better, and I certainly wasn't in charge of it back then. Now that it falls on me, I don't know what I'm supposed to do, so I'd appreciate some help on this, please.
I recommend you to set up a test system and gain some experiences. It can be a copy of your production system. Use that system to evaluate changes. If they break something, repair it or reinstall it. If everything works, apply it to the production system.
And very important: Read the documentation of the systems you're working with. Try to understand why your successor did what he did. It's not that hard to run a small web server, there's lots of help out there. If you have more precise questions, come back here and we'll help you. But "How do you set up a public website on a Windows server?" question is very broad question.
As for wwwroot: What server are you using? IIS? Why do you think it's bad to put the whole page directly into wwwroot?
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If your server is already running as it should be, I suggest you don't change anything in it.
Otherwise, you may need to hire a Windows admin. You have to be careful before changing anything on production servers especially if you don't have the required experience.