Unclear documentation on putting Iodine behind another nameserver

I'm trying to get Iodine working again after changing servers, and I'm unable to figure out what setup I had before this. I'm running BIND on port 53 and Iodine on port 54, and in my named.conf I have two zones: t1.example.com for Iodine, and then example.com for all my other stuff. The t1 zone is forward only to 127.0.0.1 port 54, but I can't get Iodine and BIND to work together properly. What am I missing here? The documentation on this setup is pretty vague, but I can't out Iodine in front of BIND because I need zone transfers to work.

Using different ports is a very complicated setup and not recommended. You would have to make sure that all replies are routed the right way back. One way could be to use firewall rules to divert DNS packets containing the tunnel domain to a different port (I think the suggested working way for this was lost, see https://lists.wpkg.org/pipermail/iodine-users/2015-March/000411.html)