I found that if I add

ul.rMenu li {
position: relative;
left: 75px;
}

...I can move the menu bar over to the right to center it. Problem is that the drop down child menus don't line up with the parents. They end up being over to the right, beneath the parents. How do I change this so that they open directly beneath the parent?

It's better to use %page-center for a centered menu.

That seems a lot simpler than the other suggestion. Where would I place that code to get the desired effect?

ata > style & edit header area

you can do most of the things you would want with atahualpa right out of the box
as well as most info is provided in the many examples inside the theme options pages