The thing that I like best about Atahualpa is that 99% of the time anything you might want to change is right in the theme options (unless you are looking to run your sidebars across the page horizontally or something else truly exotic). However that can be a two edged sword. Sometimes you can spend a lot of time building a color scheme only to realize you don't like it and need to start all over. This is not much of a problem if you are only building one site but becomes a problem when you are working on a lot of sites.
Please share any tricks you have developed to set the colors quickly in the theme options.