Having a server with these administrative tools is not a trivial task, watch out for these issues:
Iptables problems everywhere
Docker creates it's own rules, but also does WHM.
So every now and then WHM erases docker rules, meaning you either have to restart docker service or create a script to recreate the docker iptables rules.
Web Server war
If your docker containers have web servers (say apache, nginx,for instance) you'll probably have conflicts using ports, as your server is more likely to be running its own apache instance.
Docker service restarted, problem?
Sometimes, WHM restarts services or something like that. Be aware that this also restarts the docker service, which is running your precious containers.
If any given container was not created with the "restart always" option, it will not automatically restart and you'll have a bad time.