First no you didnt loose control. If you dont have a firewall than any open ports are open.
Second of all, I know this isnt a quick fix for you but...
Ive been struggling with trying to understand iptables too since I recently installed Debian and recompiled my kernel as 2.4.22. Anyway, I would say that if you have ftp installed on your system it is probably open for attack. I dont know much what commands to use to check for what is running on your box so just google around.
Finally, Im not sure what you mean but you can install your own iptables once you know how to use them. There are of course many to look at and try to understand yourself just google iptables.
Good luck. I find it tough too.