By default the RSS link in the logo area of my site links to mysite.com/feed. I want to change it to feedburner. I have gone to the RSS settings in the atahualpa theme settings and configured everything for feedburner, however this only seems to affect the widget that I can put in my sidebar, not the one that's up in the logo by default.

I would also like to enable the subscribe by email feed, though again setting the icon display to "yes" in the atahualpa theme settings only seems to effect the sidebar widget, not the logo area.

What did you use for the ID? Make sure it is as described in the Atahualpa RSS section.

I used my feedburner URL as my ID.

You should just use the Feedburner ID which is generally the last part of the url such as if your FB url were www.feedburner.com/mysite the id is mysite. The instructions in the Atahualpa theme options explain that further.