It's common to want to do Network Address Translation (see the NAT HOWTO) and packet filtering. The good news is that they mix extremely well.
You design your packet filtering completely ignoring any NAT you are doing. The sources and destinations seen by the packet filter will be the `real' sources and destinations. For example, if you are doing DNAT to send any connections to 1.2.3.4 port 80 through to 10.1.1.1 port 8080, the packet filter would see packets going to 10.1.1.1 port 8080 (the real destination), not 1.2.3.4 port 80. Similarly, you can ignore masquerading: packets will seem to come from their real internal IP addresses (say 10.1.1.1), and replies will seem to go back there.
You can use the `state' match extension without making the packet filter do any extra work, since NAT requires connection tracking anyway. To enhance the simple masquerading example in the NAT HOWTO to disallow any new connections from coming in the ppp0 interface, you would do this:
# Masquerade out ppp0
iptables -t nat -A POSTROUTING -o ppp0 -j MASQUERADE
# Disallow NEW and INVALID incoming or forwarded packets from ppp0.
iptables -A INPUT -i ppp0 -m state --state NEW,INVALID -j DROP
iptables -A FORWARD -i ppp0 0 -m state --state NEW,INVALID -j DROP
# Turn on IP forwarding
echo 1 > /proc/sys/net/ipv4/ip_forward