I am currently uploading my new test site to a folder on my current website <www.proserver.com/newsite> but now want it to go live, if I point the uploads to <www.proserver.com> it will override some files with the same name in my current site, I would like to keep their integrity intact
Using a 301 redirect I think is the way to go for this.
Create a .htaccess file with the below code, it will ensure that all your directories and pages of your old domain will get correctly redirected to your new domain.
The .htaccess file needs to be placed in the root directory of your old website (i.e the same directory where your index file is placed)
Options +FollowSymLinks
RewriteEngine on
RewriteRule (.*) http://www.yourdomain.com/newsite/$1 [R=301,L]
Please REPLACE www.yourdomain.com in the above code with your actual domain name.
In addition to the redirect I would suggest that you contact every backlinking site to modify their backlink to point to your new website.
Note* This .htaccess method of redirection works ONLY on Linux servers having the Apache Mod-Rewrite moduled enabled.