The configuration for clamav and spamassassin is in /home/admispconfig/ispconfig/tools
But the main problem might be that ISPConfig runs spamassassin not trough spamd. You can try to patch this, If i remember correctly there are some threads in the forum about that.
I also have some troubles with iptables. I have a customized iptables and plan to use it for the system. But after a few minutes/hours (?) anything changed it to a default iptables. I think Bastille-Firewall does this, but I can't also find where this default iptables is. If I find it, I can also replace it with my own.
You can deactivate the ISPConfig firewall and setup your own firewall rules manually.