Hi, I have Bootstrap 3 and am trying to apply the Slate theme, which is dark. When I choose options, it says it is applied, but when I go live, it is not applied. Also, unless I manually attach a Theme CSS file in the middle panel, nothing is attached.
screencast.com/t/bToQzIO0nfGq
Also, there doesn’t' seem to be any instruction on how to choose the various color options within a theme.

Hello,
The theme field should actually stay blank. Bootswatch replaces the original bootstrap.css file with the selected theme's css file and this is not related with bootstrap files include options dialog.
Please make sure your dreamweaver site is properly defined and you are previewing the right file from your local testing server.
What do you mean by "the various" color options? Each theme has its own styles applied over the original bootstrap styles. That's the point of this extension.

okay, what I found out is that it did not updated the header to use css/3/bootstrap.MIN.css (My capitals). That was the problem. I added this manually and it then showed the right css layout. This was a repeatable failure.

As to the various... you see in the preview multi sizes and color bottons on the theme, but no instruction on how to select the variants...

The various sizes and colors of the buttons can be changed in the bootstrap 3 elements inspector panel, as it is described in bootstrap 3 elements documentation.