If you have set your Application vault install with a URL path of /wordpress for example you with would be live at mysite.com/wordpress. If you wish your site to be live at www.mysite.com you will need to change the URL path. You can do this in your cp.magnethosting.ie control panel under:
Websites >> Domain name >> Web Applications >> Click on the WordPress application you wish to change the URL path on >> Click on the Change URL Path >> URL Path remove /wordpress >> Submit
The same would apply for Joomla and any other application that the URL path needs to be changed on the Application vault install.