My question is regarding security. Do I need to set up multiple instances of SSRS on the server, one for each application that will be using it? Or, can I handle all security within SSRS and roles so that I can ensure access is not given to another
applications data?
It is not necessary to set up multiple instances of SSRS. A single instance will work however you need to provide role and permissions to different users accessing the SSRS.
Authorization is based on roles that you assign to a principle. Each role consists of a set of related tasks, which are in turn composed of related operations. For example, the
Manage reports task grants access to the following report server operations: view reports, add report, update report, delete report, schedule report, and update report properties.
Refer http://technet.microsoft.com/en-us/library/bb522824.aspx
Regards, RSingh