The best way to accomplish this is by setting up multiple IP addresses on your host computer, one for each client/customer. You can then instantiate an EMS for each IP address. The only thing you need to do is, in the config/config.lua file change all of the IP/Port bindings from 0.0.0.0 (which is any destination address) to the address you wish that instance to bind on. You can leave all the ports the same, with the exception of the ascii interface port.
This allows you to setup as many "virtual hosts" as you like, each one having its own configuration. If you want to set bandwidth or connection limits per customer/client, you can do that via each config.lua file.