WP Empire Builder will still work, it's just that it cannot create directories, subdomains and addon domains automatically. Those would need to be done manually.
Any (sub-) domain you add should be mapped to the same folder where your main site is installed. This is not a default value so pay attention to setting it carefully.
For example, if WP Empire Builder is installed on a domain called EmpireBuilderDomain.com then every time a subdomain is mapped manually, it should be added like this:
And not subdomain.SomeOtherDomain.com
Article ID: 136
Category: WP Empire Builder