Issues with creating databases using Multi-DB plugin


I am working off of a vps server for multi-db, and I created two separate packages for my domains. After following the wpmu steps as the root user, I created multiple databases. However, they did not appear in the cpanel in which that database was created for. I have waited well over 24 hours for apx 267 DB's. So my question is, am I creating database to my local host server, or do I select that database that appears on the left first, and sql inside that base? But wouldn't that create databases inside my main DB that's running Wordpress?