With RDS you can have up to 40 DB instances running, each one its own isolated environment hosted on AWS. Multiple databases can reside in each instance and can be created and maintained through an API, the AWS command line, or the browser-based console UI.
There are some limitations with how the 40 instances can be split up due to licensing, including a maximum of 10 for Oracle when using the license-included model and 10 for each of the four SQL Server variations under a similar type of license model.
No matter your particular RDS configuration, there is always a master user account tied to each instance that has full control of all databases within.