lammert - 5:03 pm on Feb 25, 2012 (gmt 0)
Sorry for the delay, I hope that I'm not too late :)
Shorewall is a front end for the standard Linux iptables firewall. You can find the configuration files in the /etc/shorewall directory. The file /etc/shorewall/rules would be the best place to add your exception rules to allow webmin and pop3 traffic.
Shorewall has a website [shorewall.net] with a lot of documentation and examples.