Well, just try it.
tc -s qdisc will give you statistics where cake reports how many packets traversed through the different priority tiers, so just run a test and see whether the correct counters increase.
Typically on a wan link's ingress side qdiscs run before iptables got hold of the packets, so on ingress the marking most likely is not going to have an effect on egress it might (unless the NAT system had to re-map the ports to different internal port numbers)...