It looks like you solved #1.
For #2, try adding this to your Ataualpa Theme Options > Various Content Items > Add HTML/CSS Inserts > CSS Inserts:
The first rule fixes (or sets) the position of your header to the top of the browser. The second rule pushes the main content down so it's not hidden by the header. The last rule fixes the position of the sidebar.
The problem that you'll find, though, is that the sidebar is going to hide your content on smaller viewports, like mobile phones, even without the above modifications. You can see what I mean by narrowing the width of your browser. That's because Atahualpa is a fixed width layout using tables, and it's very hard, if not impossible, to make a table layout "responsive" (i.e., change the layout depending upon the width of the viewport).
Since it looks like you're just getting started with this particular site, you may want to try the Montezuma theme, which was created by the same developer as Atahualpa. It was designed from the beginning to be responsive. There is a bit of a learning curve to the theme, though. Like Atahualpa, it is very customizable, but instead of using option pages, you'll have to learn how to modify what are called virtual templates and virtual CSS files. To get a feel for how customizable the theme is, take a look at the sites in the Showing Off thread in the BytesForAll forum. You can also do things like fixing the header to the top of the browser in Montezuma as well, it's just a matter of using a similar type of CSS rule that I posted above (you should basically be able to do the same thing with just about any theme).