Have you taken a look at Controller Renderings in Sitecore MVC? These give you the ability to map a controller class to a Sitecore presentation item that can be statically or dynamically bound to your layout details.
This post has a reasonable overview of how to get started with controller renderings.
As for specifying the location of View files for multi-site environments you can pass the path to the razor file into the Controller View method, for example:
return View("~/Areas/SampleArea/Views/SampleArea/Index.cshtml");
I hope this helps.