By associating the entity, that is containing the user-specific data, to the entity System/User, which is the useraccount. In the entity limit access to the currentUser by adding the xpath to
[YourModule.EntityWithUserSpecificData_User = '[%CurrentUser%]']
Now, when you do a retrieve of 'EntityWithUserSpecificData_User' the app will only show the objects of EntityWithUserSpecificData_User that are associated with the CurrentUser.