How to run a subdirectory multisite install under a subdomain

This has been solved, please note I am using WordPress 3.8 at the time of writing this, if you are from the future these plugins may not work with your current version, please check compatibility first.

The plugin WP Multi Network provides this functionality. It basically allows you to create nested multi-site networks. I have my primary network at domain.com and created another network called Clients at clients.domain.com.

Now domain.com points to my main site, but any subsite I create from the Clients network will take an URL in the format clients.domain.com/sitename/. All networks share the same database.

I used the standard wordpress subdirectory multisite configuration for Nginx (http://codex.wordpress.org/Nginx) and use the plugin Nginx helper to generate my map{} rules.

I hope this helps anyone else who has this issue. You can now create multiple multisite networks at different subdomains (or different domains) sharing a single database and administration panel.