activate iptables rules on a bridge module installed debian machine

We use debian 3.1 to accomplish a firewall application. We use
iptables (1.2.11 default installed on debian) and bridge (erhernet
bridging-1.0.6). We can configure bridge utulities and we can use it
as a transparent machine on our network. But we want to use iptables
to restrict the network traffic. We use this system for restrict the
p2p programs on our network. We can't activate the iptables rules on
this machine. We can see iptables rules but it cant work as we want.

Help me if you can! .... :)

Best Regards
Ugur Buyukdemirci
Osmangazi University /Turkey