Thanks for this. I found that the local site name was hard coded in the CSSMenuWriter menu.php file:
$WA_localRoot = "/site_name/";
$WA_remoteRoot = "/site_name/";
So I changed it to this which fixed the menu issue:
$WA_localRoot = "" .$WAGLOBAL_localRoot ."";
$WA_remoteRoot = "" .$WAGLOBAL_remoteRoot. "";
The site name was also hard coded for the URL location of all the images used in the CMS, this was rectified by changing the URL path for each image.