Positioning can be done by using this as the layout. Make sure you clear your jat3 cache. Looks horrid though as it needs a lot of re-styling.
<?xml version="1.0" encoding="utf-8"?>
<layout>
<name>Default</name>
<description>Default layout for JA Anion template</description>
<blocks name="top" style="xhtml">
<block name="mainnav" type="mainnav" markup="3"></block>
<block name="header" type="header"></block>
<block name="cpanel" type="usertools/cpanel"></block>
</blocks>
<blocks name="middle" colwidth="20" markup="3" fixheight="1">
<block name="content-mass-top" style="raw">content-mass-top</block>
<block name="content-top">content-top</block>
<block name="inset1" width="20">left</block>
<block name="right1" width="30">right</block>
</blocks>
<blocks name="bottom" style="xhtml">
<block name="botsl" type="spotlight" markup="3">user5,user6,user7,user8</block>
<block name="navhelper" type="navhelper" markup="3"></block>
<block name="footer" type="footer" main-inner="1"></block>
</blocks>
</layout>