I donot have a my.cnf file. I have hard coded values for msl to log slow queries in mysql.server script.

Code:
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.
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'start')
# Start daemon

if test -x $bindir/mysqld_safe
then
# Give extra arguments to mysqld with the my.cnf file. This script may
# be overwritten at next upgrade.
$bindir/mysqld_safe --log-slow-queries=/usr/local/mysql/logs/ --long_query_time=2 --datadir=$datadir --pid-file=$pid_file >/dev/null 2>&1 &
# Make lock for RedHat / SuSE
if test -w /var/lock/subsys
then
touch /var/lock/subsys/mysql
fi
else
echo "Can't execute $bindir/mysqld_safe from dir $basedir"
fi
.
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code

MySQL will not log em.

Do I really need a my.cnf file or is there a way to work with the above code

You need to use a file not a dir

--log-slow-queries=/usr/local/mysql/logs/slow_query_logs.logs

Thank you.

Worked like a Charm