I went through this a couple of times. I installed the component, applied the patches then moved onto Manage Site/New. The screen that shows up at that point is very different than what is in the manual. None of the database information for the main joomla installation is populated. I continued on with the installation, all the compatibility checks are fine, but then at the database set it is failing saying Could not connect to the database. Connector returned number: Unable to connect to the database:Could not connect to MySQL

I am able to connect to the joomla database from the command line without any problems - I don't understand why the component is not being able to connect. Are there any other permissions that I need to look at? joomla/configuration.php has the following info for the db connection and the main site was connecting with that just fine before I tried to set up multisite.

var $dbtype = 'mysql';
var $host = 'localhost';
var $user = 'root';
var $db = 'joomla';

Pretty frustrating. Not to say that after this I had to manually back out the component to get the main site to be functional again.

The screen that is display depend on the context.
In the user manual, we used the context that display alll the parameters.

To have DB parameters available when you create a SLAVE site, you have to define the replication rule. The replication rules are defined in a "website template".
Therefore, start to create a template in which you will define the replication rule.
After that, you can create your slave site using the replication rule and specific a new table prefix. This will replicate the website in the same DB than the one specific in the replication rule.

In you post, there is something that is not clear.
You speak about the main site (master webiste) but you say that you use "manage site".
If you have "manage site", this mean that you are connected on your main site and that the problem is to create a slave site that replicate an existing one with new table prefix.

When you create a slave site without new DB prefix, this create a "fresh" slave site that need to use the Joomla Installation.
Go on the slave site domain and it will show you the Joomla installation procedure.
There you will be able to define your DB parameters.

I suggest that you have a look in the video present in the tutorial to understand the concept. Follow it step by step. It works like a roadmap that will guide you on the step to apply depending on your particular case