You need to check through the various settings and start to get familiar with them. There are over 250 settings and sometimes there are several ways to accomplish what you want.
The theme setting you currently have are from the theme style that is installed by default when you install Atahualpa to show you some of what it can do. You change the style as described in the FAQ thread.
Specifically this post.
You can alternatively make changes in the CSS of your site in ATO>Add HTML/CSS Inserts>CSS Inserts and other "Style" sections of the theme options.
For example to change the height of the header image you go to ATO>Header Image or you could go to ATO>Style & edit Header Area and change the logo area styling.
As you can see there is often no one way to do something.