To fix your double-margin issues, use display: inline; (where ever you’re using margin-left). To fix some of your other issues, IE doesn’t take kindly to negative values (i.e. top: -775px;). For this, you need to make sure you’re using code that supports all browsers, so re-coding the main page might be in order (or at least the top part) to help IE6 read your code properly. By having the pop-up saying "IE6 is no longer supported, you could use an update" shouldn’t need to be there as compliant code should work in all browsers. As a developer, you need to make the code work for all users (not to mention that 22.3% of internet users as of September 2008 use IE6, http://www.w3schools.com/browsers/browsers_stats.asp).
I am not trying to degrade your work, but rather to inspire you to make sure those viewing your site have a good experience.
Like I said above, look into the IE double-margin bug, and negative value fixes.
Hope this helps,