I was afraid this application would be beyond my skill level.

I was following tutorial #16. I had created a salve site#1, then created a template off that slave site. When trying to create new slave site with the template, I recieved many error messages. So, I decided to delete this new slave in the site manager. When I did this, everything in the entire www rooot directory was deleted with the exception of the multisites config file located in the master joomla site directory I had created. I lost directories and files that had nothing to do with joomla and/or JMS.

Fortunatley I did not have any live sites - but I have lost a lot of efforts on "dummy" sites I was using to learn how to use Joomla and now JMS. I don't understand how this could happen. These other directories had no association with JMS. (at least I thought).

At this point, I feel I may be afraid to move forward in trying to use this product in fear of loosing everything once again.

All depends on the deploy folder path that you have used.
Normally, when you deploy a slave site into a specific directory, when you delete it, you just delete this directory.

You have specified the master website directory into the slave site deploy folder then this may explain why you have deleted you rmain website.

If you have specified the "deploy directory" = {site_dir} this normally create separated directory and therefore when you delete it, you will delete this specific directory.