Once you are satisfied with your security configuration, you may want to make it the default configuration for all ES servers (if it isn't already), or make it the security configuration for MFDS as well.
To make it the default ES security configuration, go to the Security options in MFDS, then to the Default ES Security tab, and follow the instructions listed above for creating the security configuration.
To make it the MFDS security configuration, you can either do the same on the MF Directory Server security tab, or, if you have made it the default ES security configuration, go to that tab and select the Use default ES Security Manager List option. Note that MFDS security is somewhat more complex than ES security, and consequently you're more likely to run into configuration issues with MFDS.