Unfortunately in order to even begin to help we'll need a lot more information. Try giving us a sample of the CSS and HTML that's not working, and describing exactly what's different between IE6 and Firefox.
Hi there, in my experience the problem is how browsers define their measure units. Try to eliminate all the margins in the CSS and use more images for your layout to have a more accurate version for both IE6 & Firefox. By the way, IE7 and Firefox show the websites in the same way, so if you fix your project for Firefox you will cover three different browsers: IE6, IE7 and Firefox. Also eliminate all the "heights" in the HTML code that will help too