Ouch! Basic home page is displayed all wrong in IE
Do you have link to the site so people can see the issue? Probably is css issue as you suspected, specially if you are using absolute positioning.
looks like you're talking about the CMS not working in ie6. That's desired behavior.
plain yogurt (or any other theme you put the love into) should be able to render for your site visitors in ie6 just fine though. No?