Proper Iptable configuration file

[Kihara Muriithi]

Hi all,
  I am seeking advice of which file one should ideally edit if one
need a configuration that system-config-security script (in Redhat &
Fedora) can not handle. I am aware one can edit iptables directly, but
all changes would be lost on reboot or if one adjusted security
through system-config-security script.
 What is the proper way of doing it?

Thank in advance
William
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