WHM showing one domain on shared address

You need to be a bit more explanatory with your question. But what I make out from your question is that main domain shows up when you goto any domain on the server. (hopefully I have not misunderstood you) . In that case you need to check if all <virtualhost> entries are present or not and you must have "NameVirtualHost xxx.xxx.xxx.xxx:80" specified before the first virtualhost in httpd.conf