g1smd - 8:27 pm on Apr 7, 2013 (gmt 0)
Moving the files around on the server, into some sort of structure, makes life tidier for when you're working on the site.
If you simply move the files, then yes each page will have a new URL. However, you could add an internal rewrite so that the old URLs continue to be used. The rewrite connects the old URL request to the new internal file location.
However, it sounds like you do want to use new URLs too, so you'll simply add a redirect (using a RewriteRule) for each page URL at the top of the htaccess file and make sure that all internal site links point to the new page URLs.
The redirect is for people clicking stale SERPs and accessing stored bookmarks as well as to inform searchengines the page has moved.
These redirects are VERY easy:
RewriteRule ^oldpath/oldfile.ext http://www.example.com/newpath/newpage.ext [R=301,L]