Lately I'm playing a lot with WSS and MOSS. It wasn't really clear for me what the difference is between a web application, a site collection, a site and a sub site. This is what I found out. On top of the hierarchy is the web application. In technical terms, this is a web site in IIS (with an application pool associated). A web application needs to have at least 1 Site Collection. The Site Collection is the root site of the web site. Below the Site Collection, there can be one or more Sites. And a Site can contains sub sites.
An overview:
1. Web Application
1.1 Site Collection (SPSite)
1.1.1 Site (SPWeb)
1.1.2 Site (SPWeb)
1.2 Site Collection (SPSite)
1.2.1 Site (SPWeb)
1.2.1.1 Sub Site (SPWeb)
1.2.1.2 Sub Site (SPWeb)
The words between ( ) are the objects of the SharePoint API.
Backup
You cannot backup a web application from within SharePoint. But what you can do is save the configuration in IIS.
With stsadm.exe -o backup -url <site URL> -filename <filename> you can create a backup of a site and all sub sites. And you can restore it with stsadm.exe -o restore -url <site URL> -filename <filename>.
As far as I know there is no built-in option to backup or restore a sub site of SharePoint.
Web Applications
In my case I created three web applications. One for my private SharePoint, one for my blog (new blog soon) and another which allows anonymous access, but IP-filtered. Because each web application of SharePoint is a web application in IIS, you can setup all the security properties of IIS, like IP-based security.
Hope this helps,