Create a footer menu from primary links and should be able to control what should appear I have a menu at the top on hover it expands. I want a menu at bottom of page with same links, but i may choose what should appear here. Is there any module available for it.
For this functionality, try Footer Sitemap

It allows you to choose which menus and/or menu items will be included in the footer sitemap.

You can then customize the template included to manipulate the markup if you need to.