Are you trying to put the Google AdSense search in the sidebar, in the main section of the index page, or in a post? Generally, when you're using JavaScript -- which most AdSense relies on -- you'll need to put it into the sidebar.
(I've had some luck putting JavaScript into posts by putting the code into a table... I talk about that in my book about Branford Magazine.)
However, have you seen Michael Oeser's newest theme (in beta as of mid-April 2008), called Wynton Magazine? It includes an advertising section in the middle of the homepage.
http://wp-themes.der-prinz.com/wyntonmagazine/
I haven't tried that theme yet, to see what it does, but it may include some useful code for your purposes.
(For the record, Sites that Soar! -- the book that I co-authored -- does not offer help with Google AdSense. It's strictly about the basics of installing and customizing Branford Magazine and Mimbo, though I make a brief reference to using tables in posts, for JavaScript references.)