Moving code to improve SEO

Hello,

I am in the process of setting up a small website using Atahualpa, and am learning about SEO.
From what I understand, it's important to have the content of the page above things such as menu code so the web crawlers get the content.
Have had a look at the source code of my landing page and there is a section of code for the JQUERY which is 106 lines long (line 40-146).
I am looking to move this code to beneath the web page text, how do I do this?

I'm using Wordpress 2.9.2 & Atahualpa 3.4.6.

Sorry if this is the wrong Area to post this.

Thanks, Andrew