I setup and MVC 4 application and added authentication against our Azure AD server as outlined here: http://msdn.microsoft.com/en-us/library/windowsazure/dn151790.aspx
A
First, tokens returned by Azure AD do not currently contain claims for roles or groups, so you need to get them from the Graph API. Second, roles in Azure AD that are returned by the Graph API are not necessarily intended for use in an ISV/LoB app, and in general you should use security groups for authorization instead. To perform authorization, you should use the checkMemberGroups or getMemberGroups operations in the Graph API, which are transitive and valid for this purpose.
If you check out the following resources in order, I think your questions will be answered. You'll learn how to authenticate to the Graph, call it, and configure your application to use the result of the group operations to perform authorization: