I have a Website built on Joomla 2.5 and have recently installed Virtuemart 2.0.12b and everything is great except when I am in the shop and click in to view products my top main menu dissapears. I notice that the URL changes also, but I am confused as to how I can assign my shop to the menus.
You should assign a main menu item to the VirtueMart Front Page - or whichever VM option suits you best, and then make sure that you assign your main Joomla menu module to that item using Joomla's module manager (although normally it would already be set to show on all pages that are associated with a menu item).
See ther Joomla docs: http://docs.joomla.org/Help25:Menus_Menu_Item_Manager_Edit