changing folder domain points to- wp issues?

I should have set my hosting structure up correctly to begin with, but didn’t think I’d want to host more than one site at the time I started the hosting account. Now I’m not sure if I’m going to have issues or not…

Basically I can host as many domains as I want on my one hosting account. However, they all share the same root folder. Extra domains are pointed to a folder within the root. Now that I’ve added a new domain I am going to have duplicate content issues if I don’t change my structure.

Currently I do not have WP set up in the root, I have it in its own directory with a few static pages in the root. They all link together.

I set up another folder to point the second (new) domain to. The issue is, if you go to my mainsite.com/folder-of-second-url the content for the second url is visible there, as well as at newdomain.com (major duplicate content issue!)

I would like to add a few more sites to this account and need to get my structure fixed before doing it.

The hosting support said if I pointed my main site to a folder within the root, it wouldn’t have the issue of the mainsite.com/second-url content showing up as they would be separated.

So my question is this: If I point my main url to the current wordpress folder (which works as I was getting ready to delete my static pages and have wp as my full site anyway) will there be issues with wordpress in the database write path or other areas that I should watch for?

If possible I don’t want to change the current wp setup much as I finally am getting good serp on it for my local business.

current setup:

root (main static pages and current root of main url)
—/photoblog (wp install)
—/extra (root of second url)

desired setup:

root (empty except for site folders)
—/photoblog (wp, main url root)
—/extra (root of second url)

I hope this makes sense!