My site is not working in google analytics for some reason. I put the html file in the root dir as Google suggested. Now my UA number appears to be wrong as well.

Does dropping the html file in the dir work with Atahualpa and WP or do I need to add the code in the footer.php?

Thanks!

You can add the code at Theme Options -> HTML/CSS Inserts -> HTML Inserts: Body Bottom

This is for the actual analytics code.

The "html in the root dir" code is probably some other code that Google wants you to put up to verify that the site is yours

Actually, you can skip the html file option and put the Google code in the A Theme Options -> HTML/CSS inserts -> HTML Inserts: Body Bottom.