You can get a single simple Mono web app running with one line of configuration code, but to have more control and multiple sites you should get into the VirtualHosts files. Virtual Host files aren't hard and the sooner you start the more ready you'll be when you *need* their power.
Apache "Modules" are like ISAPI Filters. Install them, tell Apache that you want to use them and on what sites, enabled them, they start intercepting requests. Mono itself is a module, your previous one-line installation made it available and enabled Apache-wide so you're just one nano away from ASP.Linux.
Sites in Apache, just like sites in IIS, can be set up and selectively enabled/disabled.
This page shows the details of getting it all right