"How do I configure properties of database connections defined in RapidMiner Server"
Database connections can be defined in RapidMiner Studio or be defined in RapidMiner Server and used by RapidMiner Studio when it connects to the server.
To define a database connection in RapidMiner Server via the Web interface, go to Administration > Database connection. Then create or edit a database connection and click on Advanced settings.
Please consult the documentation of your JDBC driver and database which properties can be configured and what meaning they have.