lammert - 1:13 am on Mar 14, 2010 (gmt 0)
First of all welcome to WebmasterWorld!
I haven't used Virtuozzo panel in the past so can't comment on that, but on Centos the site source scripts are normally stored in the /var/www directory tree. With one site on the VPS it is probably in /var/www/html, with a VPS capable of multiple sites it may be another subdirectory within that tree. Settings for the Apache webserver are in /etc/httpd/conf, but you will probably manage those settings in Virtuozzo, rather then editing the config files directly.
The safest way to transfer the MySQL database is to dump it to an SQL text file, and then upload it again via the control panel. Be sure to only remove your files and data from your shared hosting account when everything is running fine on your new server.
Parallels, the makers of the Virtuozzo control panel have a number of downloadable user manuals on their website. You can find the manual for your specific setup by choosing the product which is installed on your VPS from the Products menu, and then click on the Documentation link in the side menu.