Find the /nagios-plugins/config folder and in there you will find several files in which you define commands. I would suggest creating a new file there naming it for example user_check_sql.cfg, just in case upgrading Nagios would replace files in there. Copy and paste one command definition from mysql.cfg to your user_check_mysql.cfg file.
When you edit the user_check_mysql.cfg file, check the arguments after command beside command_line part. There you can put the switch -P
Example how it should look like for port 13306:
command_line /usr/lib/nagios/plugins/check_mysql -H $HOSTADDRESS$ -P 13306 -u username -p password
Then use the command_name in the service definition when defining check_command