This must be a problkem with the software that you use in the site and not ISPConfig, as this error message is neither from apache, php nor ispconfig.
Maybe the software you use does not support multiple domains or it needs some kind of special configuration.
I am used to ispconfig2 and am having a hard time trying to get ispconfig3 configured
First, ISPConfig 3 is much easier to setup but its diffrent then ISPConfig 2 as it is made for multiple servers and not single servers. Also there is no reason to switch to ISPConfig 3 if you dont run multiple servers as server farm.