After upgrading to CB 2.0, I've noticed that theres only one template, "Default"

Correct, the plan is to develop a plugin that allows easy generation of new templates in any color scheme you'd like from our custom LESS files, but I've no idea when I'll get around to that as I'm not making any plans until current plugins are upgraded.

How does the template system work in relation to the new Canvas Layouts?

Template system has nothing to do with that, but the PHP file of the template does, which contains preparing the HTML for the canvas positions.

How can I create my own template so things wont get overridden with updates???

Same way templates have always been created for CB.

The old templates are still in "components\com_comprofiler\plugin\templates" (bootstrap, dark, luna, etc...) Should they be deleted, or leave them there?

They should have uninstalled when you installed CB 2.0. Otherwise yes you can delete them.

Are the files in the new 2.0 default template directory new? If I want to create my own template, should I copy that directory?

Yes, the default template is 100% installable. So you can copy it, rename it, adjust its PHP file as well as XML file and you should have a new installable template. Note the template element (e.g. "default") is included in the PHP files class names so you'll need to adjust the PHP file.

With the files in the directory "components\com_comprofiler\plugin\language\default_language"...Are these the only files being used for CB 2.0...
admin_language.php, default_language.xml, language.php? So I would only need to copy these to make my own Language Template?

Yes those are the only 3 files needed for a language plugin. If you copy its folder, rename it, and adjust the XML file it'll be installable.

Can you do module and component overrides in Joomla's Template Manager with the CB 2.0 files?

For now you can only do template overrides for our Modules. We'll probably have component template override available in CB 2.1 or in a later release.

The new positions that are available for the canvas layout... Can they be adjusted, or are we limited to the positions that are supplied and just be able to change the CSS styling for the look.

No, the canvas positions are not adjustable. They need very strict CSS and coding for it to be as flexible and responsive as it is.

For example the "Canvas Main Left" column is about 15% width, "Canvas Main Middle" column is about 70% width, and "Canvas Main Right" is about 15% width. So wondering if the widths can be adjusted.

Not without altering the PHP of the template and also the jQuery in the templates PHP file to handle the column size swapping.