Visual Studio 2008 App_Data中的数据库与Server Explorer数据连接之间的区别

I've recently starting learning asp.net and MVC and would be grateful for some clarification on working with data in an application. More specifically, what is the difference between adding a new sql server database item to the App_Data folder and creating a database connection in the Server Explorer window? If I add a new database in the App_Data folder am I still able to work with this database in SSMS or I can I only work with it through Visual Studio?I've recently starting learning asp.net and MVC