The 7 minute rule got me -
What you're seeing now is the default_template, which suggests that you haven't copied the files from includes/templates/classic/css to includes/templates/mystore/css
You're on the right track. Once you have the 'classic' css file in your template, do the #logowrapper thing.
Here's the idea. When Zencart creates the pages your customers see, the first thing it does is look to see what template you've selected in Admin (in your case, mystore).
Then, as it creates the various pages, it looks in your override folders (all named mystore), if any, to see if you want to do something other than the default behavior.
If you have a stylesheet.css in your includes/templates/mystore/css folder, Zencart will use that to style your cart. If you don't, it will use the stylesheet.css file in includes/templates/template_default/css folder.
Easy, once you get the idea.
The 'classic' template is just an example template the developers provide to show you how the overrides folders work.