How to setup base domain website NOT site admin AND keep base domain name

Maybe this is a rookie Multisite question but we registered a domain name say http://multisite.com and had a VPS server setup using this domain name and installed WP then enabled Multisite.

So on the "main website" http://multisite.com" we want a website like Edublog.org to advertise and sell our services and we are going to use different themes than Farm100 and plugins like Gravity Forms.

But when we enable on the site admin they are enabled for non-supporters etc..

So I suspect the answer is using a different WP install for the base site so we have freedom to change/update themes plugins without affecting our network... correct?

If correct is it easy to rename our entire site something like http://network.multisite.com so we can move the base http://multisite.com to another web server?

Maybe there's a better way?