My host uses cpanel and something called simple scripts to install joomals and other programs. I just click and it installs it. In the video it shows your renaming the table prefix to master_ and selecting a DB name. I don't get to choose these as it installs automatically. Is this required for JMS to work?

No, you can use any table prefix to make JMS working.
We just suggested to use the "master_" to avoid the default joomla "jos_".

As you could read in the user manual, we recommand to avoid using "jos_" to reduce the risk that you destroy your master website in case of a fresh "joomla web installer" where you would use the default value. In joomla 1.5, the default is "jos_" and this would destroy (replace) your master by a slave site.

Okay simple enough to not use the installer and just install joomla manually.

Next question I did setup a master site and installed JMS on it and other extenstion in a sub directory master.domain.com like recommneded. However the joomla installation was down using simple scripts. So I am going to delete everything off the server (not much there just a testing site). Setup a subdomain master.domain.com reinstall joomla manually and set table to master. Will I be able to reinstall JMS in that subdomain if I have the install file stile on my descktop or does it expire?

Also once I setup the master.subdomain.com as my repository. How do I setup my main domain. domain.com? What does my main domain.com become? Is it a slave?

You can install and register JMS an unlimited number of times.
So you can install it on you desktop or move an environment from production on desktop.
You will just have to register it again.

If you need to get the latest version of JMS in the same version, see the FAQ for the procedure to receive a new download ID.
www.jms2win.com/en/faq/faq-joomla-multi-sites#cat-122

Concering the "joomla web installer" that would not start.
Perhaps that the "/installation" directoy has a specific content with your cPanel instal script.
You can always use the one provided by your system.
Just keep it and don't delete it as recommended by joomla.
Rename it temporarly and when JMS has installed the patches, just re-use your "/installation" to be consistent with you specific joomla.