In my experience, I've used Amazons RDS service to create a SQL Server instance and point my connection string to that in which I'll run all of my Migrations to that database. That or you can point it to whatever SQL Server instance you have with the appropriate connection string.
You can then call update-database and have your Users / User Roles created in the Seed()
method.
FYI: You may need to configure certain ports/permissions within the RDS instance to be friendly with the Elastic Beanstalk instance. (Think about security groups)
I would also download the AWS Toolkit for Visual Studio as it'll help get you setup with the database connection string and the ability to publish straight to AWS Elastic Beanstalk.