I have just started learning DNN. I dug a little into this but I just can't change the layout for whole site. I am using Awesome cycle template as starting.
I need to redesign site header and footer. If I made change in Skins\Gravity\Home.ascx then these changes are only appearing to my home file.
I can change the CSS the way I want but I am just unable to change the base html of header in entire site. (like we do in master pages in ASP.NET or layout in MVC)
Your problem probably has to do with DNN supporting different skins for different pages.
You have to check if all pages use the same skin. I think that in DNN7 default site template pages use different skins. You can check this if you go to Edit Page -> Page Appearance -> Page skin
If you set all the pages to use the Gravity skin, then changes you make at the .ascx file will apply to all pages.
A uniform way to change the layout for the whole site is to set every page skin to 'None specified' and then only select skins from Admin -> Site Settings -> Basic Settings ->Appearance ->site skin.