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With FMGo (not local network), how can I reach the files on FMS? I guess mydomain.com/fmi/webd/ will not work.
FMGo uses port 5003 and isn't accessed at that address (that is webdirect) so that is fine.
As for hosting two web servers you would be better off setting up two different external IP addresses and routing each IP address to the right server internally. Running two web servers on the same local network is fine otherwise, there won't be a conflict between the two apache servers.
If you can't use 2 external IP-addresses, you could use a reverse-proxy on your main webserver that redirects all traffic for a certain domain and/or a certain path to another server on the local network.
If its would be the same domain with a certain path you could activate the apache-modules: proxy, proxy_connect, proxy_html, proxy_http and add in the virtual host configuration the following entries:
ProxyPass /fmi/webd/ http://<internalip_fms>/fmi/webd/
ProxyPassReverse /fmi/webd/ http://<internalip_fms>/fmi/webd/
If you would use https, you should install the ssl-certificates on the main-webserver and connect to the fms just using http (it would be useless to encrypt the data once again).
I have this exact setup running with a linux-webserver and a windows-fms, works really well
If you have a separate domain it would be: