I did a test create from the front-end of my master site. What happened next was I clicked on 'manage websites' link and it gave me a login page and the title was now the site title I put in. So basically somehow the slave site I just made, took over the master site. However, it did NOT overwrite the actual directory. The slave site did get deployed in the correct folder /subdomains/user_id/template/etc.../site_id

Looking at the list of domains, I had this in my for my domains in my template:
http://{site_url},
www.{site_url},
http://{site_id}.{site_ur}

Obviously I can see that this is a problem as {site_url} = my master site! I tried to open it up and take all that off and just put the correct deployed folder but still it is taking over the master site.

Is there something I can do? I am affraid to delete it because I'm affraid it will screw my master directory up.

----UPDATE----

I went ahead and tried to delete the slave site. It deleted it from the database and it deleted its files just fine. However, now my master site wants to run the installation. However, ALL my files and configuration with the MULTISITES stuff in there is still present. Why is it trying to install when the configuration file is still there?

---- 2nd UPDATE ----

My master site is at deployed.tangerinefiles.com which gives me the installer. If I rename the installation folder it gives me the error: "No configuration file found and no installation code available. Exiting..."

However, I can see my site AND login to the admin if I go to tangerinefiles.com/deployed.

I checked my cPanel and I still have my deployed sub-domain pointed to the right place public_html/deployed so what got messed up? What do I have to change in order for deployed.tangerinefiles.com to work again?

Buddy

This simply mean that you have created a slave site that use your current master domain URL. So now this URL is recognized as a slave.

To access your master as you could read in another post in this forum, you can either create a subdomain in you cPanel where you specify the master website "document root" directory.
So that you will be able to access your master as this subdomain is not present in the list of slave site.

The other solution consists in removing manually an entry present in the /multisties/config_multisites.php to remove the domains entry that you didn't correctly entered.
This will give you a temporary access in your master and the first thing that you will have to do will be to update the slave site definition to fix the domain values.