I did the whole CITES thing and eventually gave up. I moved from the U.S. to Montreal a few months ago and invested quite a bit of time figuring out the CITES process. I ended up talking to the Marine Biologist in DC before I gave up on the process and sold my tank out on Reef Central.
The thing you need to understand is that CITES is primarily an EXPORT control. It is intended to limit developing countries ability to chop up thier fauna and sell it. If you have an export permit, customs probably will not have much trouble with it.
Here is the good news. CITES only covers (unless I missed something) reef building (LPS and SPS) corals. Fish, softies, and anenomes are not listed. You do need CITES for clams (I had a beautiful Crocea).
You need lots of data and lots of time to get through the CITES process. At least 8 weeks. You need to know things like a statement from every importer explaining where they got the coral and proof it was under CITES export control. Most LFS's do not have this. It is held by the importer (usually somebody by LAX for the U.S.). If the sample is propagated in captivity, you need a statement from the fragger stating when it was done, and by whom. Consider that when you go to your next frag swap.
I hope this helps. I wish there were less red tape, but I also wish that reef world wide were not in such a rapid state of decline. I personal believe they should ease up on the hobbiests like us. Polution and sedimentation are killing the reefs. We are trying to grow them.
Good luck.
Bill