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You can run multiple instances of Nagios on the same machine, if you ensure that the following variables are unique for each instance of Nagios...

• Main configuration file
• Status file
• External command file
• Log file
• Log archive path
• Lock file
• Comment file
• Downtime file
• Retention file

If you are using the web interface, you will have to setup separate directories to hold the CGIs for each instance of Nagios and create appropriate script aliases in your web server configuration file. This is necessary because the CGI configuration file must be unique for each setup of CGIs, as it contains a reference to which main configuration file the CGIs should read.

One last thing you should check is your init script (if you're using one). The init script should start, stop, restart, and reload all copies of Nagios (if that's what you want it to do).