I'm running an Apache Server with multiple VirtualHosts, not to mention I understand how to produce a new VirtualHost, but I don't know, the way i can setup Mono just for this VirtualHost.

I've read I have to disable MonoAutoApplication, but I am unable to find any information about how to create it on only this VirtualHost.

Can anybody in here assist me to?

The Mono project hosts an internet-based wizard for producing mod_mono designs for Apache. You'll find the tool online here: http://www.go-mono.com/config-mod-mono/

The default is to produce a configuration apply for a brand new Virtual Host.