The Virtualization server and Production Server (Apache/Tomcat in your case)are no way linked.
The process is simple as follows,
1. The content (jsp,html….etc) of the website which you are planning to host on Production Server can be managed using Alfresco (workflow, webforms, dynamic html generation (like articles, news..etc)).
2. Once you are satisfied with the content and website look and feel (using preview option, AlfrescoVirtualization Server).
3. Now its time to deploy the contents to your remote production server (Apache/Tomcat). Once deployed there is no connection with the alfresco (even virtualization server). Virtualization server is a module within Alfresco to see how your site looks when deployed to production and no way linked to production server.
4. You can configure deployment server to deploy pages (like HTML's) to apache server and dynamic pages (like jsp's) to Tomcat.
Let me know if this is confusing or not clear
–Vijay