You can modify a theme to move the menu to the left. There isn't a theme with a left side menu for the current ATutor release, but there is one (Plone) for 1.5, if you want to look at it to see how it's done.
Plone Theme
http://www.atutor.ca/atutor/themes/index.php
Re: moving content, I don't think there is a way to get your content out of moodle in a interoperable way, so you'll will likely have to move it manually. Once you get it into ATutor, there after you can export content packages that can be used in many systems that support importing of IMS conformant content (including moodle).
You might want to suggest a moodle migration tool to the feature requests forum.
Feature Requests