You can do the subdomains thing by copying the current apache config and configuring the subdomains you want to use. The adjustment you need to do is to make sure when you proxy the /http-bind and /xmpp-websocket you pass as Host the original domain you used to install the deployment and keep the config.js. Not sure how to do that with apache.
If you want a custom config.js configuration you can copy the existing and do not change the domains there, just change the settings and have it served for the specific subdomain:
Basically, you need to just adjust only the apache configs and define each subdomain you want to use.