There is a problem with placing some third party code into the new blogger layout. If your adsense code doesn't look right when you place it manually, then you have to use escape characters to make it right.
Here is how it is done:
Trick to Add AdSense, AdBrite and Other JavaScript Ad Code Directly to Blogger HTML Template
Edit: Another Link which is more useful. A small online application to convert your code: http://www.eblogtemplates.com/blogger-ad-code-converter/