I saw in another posts saying to setup a master.domain.com and have all extensions and jms installed on this site with no content so it can act as a library for the other sites. That I understand. However, I have a site with Jomsocial installed that I paid for. Is it possible to setup all the extensions and jms on the master subdomain and remove all the content off the site domain and just keep jomsocial installed. I figure if I do this my main domain will just have jomsocial for people to use that, everything else will link to my other sites which will use other extensions and be run by JMS. However if there is no way to "move" jomsocial or make my domain a master then I can repurchase but trying not to. Can I just remove all the content off my main domain and make that a master?

Yes you can install JMS on an existing website.
The recommandation does not mean this is mandatory.

You can effectivelly start by installing JMS on the existing website and after cleanup the content of a duplicated (replicated) site.

If you just want to create fresh slave site, you can also use your current site as master. The disadvantage is that each time that you will install something that is based on a replication of the master or the install from the master, you will have the content copied.

You can also "clone" your current website to build a master that will have a slave that is your current site. So that you will have a new master as startup with the current content that you can cleanup to build the other sites.