Answer by Zoredache for What are the pros and cons to editing iptables configuration file vs adding rules via the iptables command

Most people with this situation handle it with some abstraction.

For example. Instead of having a single file with your rule set, why not build a set of files with your rules and concatenate them together.

For example you might add individual rules into files named like this.

/etc/iptables-rules/00_flush_drop/etc/iptables-rules/20_permitotherstuff/etc/iptables-rules/10_permitssh/etc/iptables-rules/99_drop

Then just run the rule set with run-parts /etc/iptables-rules. If you need to add another set of rules, just temporarily insert add a file. and then remove as needed.

You should also strongly be looking at setting up and using CHAINS in your configuration. Chains are kind of like sub-routines. You could for example add a rule at the very top of your firewall to jump into a chain. Chains have a default policy of RETURN. So when you needed to add a temporary rule, you just insert it into that CHAIN. When you you longer require it, just flush that particular chain.