Fix Joomla Links and SEO

I created a site using Joomla in a directory called [login to view URL] We have been testing it for weeks and all is well. I put the files on the live site and I am now having several problems. The site is using ARTIO JoomSEF, Virtuemart, and a few other components. When I moved the files now the search engine friendly links are not working. and several links on the home page and copy are not working. I need this fixed now if possible.