You could try Firebug lite (getfirebug.com). That will allow you to inspect the elements on the page and change things on the fly. But with IE for the most part its going to be tweaking the code and giving it a try in IE. 
Hi Justin, The problem is being caused by the side menu that I have fitted on to the index.php. How do I add a correct side menu without throwing everything else about? I put side menu as an 'experience' Div with menu writer php inside.
Also, with my side menu taken out, the rest of the site still does not want to appear correctly on IE, all I've done for the other pages is change the colours, a few minor adjustments.
Code below; -
<div id="navWrapper2">
<div id="topNavigation">
<div id="searchBox">
<form id="searchForm" method="get" action="Products_Results.php" >
<input name="Search" type="submit" id="Search" value="Search" alt="Search" />
<input type="text" name="S_ProductName" id="S_ProductName" />
</form>
</div>
<?php require_once("CSSMenuWriter/cssmw_home/menu.php"); ?>
</div>
</div>
<div id="experience">
<?php require_once("CSSMenuWriter/intermediate.php"); ?></div>
<div id="storeMessage">
<h1>Don't let vintage<br />shopping become<br />a thing of<br />the past<br /><br />Get your<br />frock on!</h1>
</div>
<div id="featuredWrapper">
