Most likely IQ Cockpit only sees one database (the first) in a server. This is the default behavior when you connect to a SQLAnywhere-based server.
If jConnect is being used by IQ Cockpit to connect to the IQ server, then the default connection URL will automatically connect to the first database started in the server.
To connect to another database in the same server requires the addition of the '?SERVICENAME=<dbname>' parameter to the connection URL. As databases even in the same IQ/SQLAnywhere server are separate and distinct, this would require some additional work to discover the second database to even construct the URL extension. As the recommendation is to only run one database per IQ server instance, I doubt this is done for IQ Cockpit.
I would suggest sticking with the rules and only run 1 database per IQ instance. As you can use the utility database (empty server) or an existing server to create the database (as you have done), you already have your database.
All you really need to do now is shut down the existing server and start 2 servers, each running the separate databases and on different ports with different names (use another .cfg file). Adjust resource parameters accordingly.
After that IQ Cockpit should see both servers/databases.
Chris