Fedora Networking :: Proper Management Of Iptables?

for quite a while inside of our organization we've been editing /etc/sysconfig/iptables directly without much issues. However it was suggested to us that by doing so we risk losing all those rules whenever some package decides to use lokkit or "system-config-firewal*"Doing a bit of analysis I can't really find any trace of code that would prevent us from maintaining iptables just the way we were (as long as *we* don't use lokkit or system-config-firewall*) since "service iptables save" is a valid technique and uses iptables-save script which is part of iptables package and *not* part of system-config-firewall*

So we've got some evidence that may confirm our usage as valid, however it would be nice to know if indeed this is *not* a recommended way of maintaining iptables and we should reconsider how we approach it.