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You can check to see if slow query logging is currently enabled. The following command assumes you have configured .my.cnf file:

mysql -e 'show variables;' | grep slow_query_log

Output should show something similar to:

slow_query_log  OFF
slow_query_log_file     /var/run/mysqld/mysqld-slow.log

There are now 2 options for configuring slow query logging. You can add the settings in the .my.cnf file or you can set the variables through the mysql command line.
If run the following command it will set slow query logging without needing to restart mysql

mysql -e 'set global log_slow_queries = 1;'

You can now run the following command and it should produce an output saying that slow_query logging is enabled:

mysql -e 'show variables;' | grep slow