If you installed MySQL from the repositories using yum, it will need to be started and stopped as root because it runs as a system service. That's going to give you a headache setting it up in Netbeans.
The commands to start and stop MySQL are, as root:
# systemctl start mysqld.service
# systemctl stop mysqld.service
I don't think you'll successfully set those up in Netbeans. Whatever plugin you are using, I suspect it really wants the mysqladmin tool for the admin tool (rather than MySQL Workbench).
What's your thinking behind setting up MySQL under the control of Netbeans?