Dear gurus. I have a virtual server with a number of domains. For PCI compliance I need on one of them to switch off the 3306 port. In another I need to change the port. On the others I want to leave them as is (open on 3306 but only allowed from given IP). 
I believe this is done in config files located in the etc folder for each domain and can be done in cPanel. 
My question is, are all these mysql ports independent per domain?  My worry is there one instance of mysql on my virtual server, and if I change the port on one domain  it’ll change it for all and mess them all up. 

Ask your host. Only they can answer your question.