Will the search engines index my top level domain with WP Empire Builder?

When you use WordPress multisite, then your new page will have TWO available urls:

your-mother-site.com/domain-name-com/directory and:

domain-name.com/directory

We use special code to show to search engines that domain-name.com/directory is the "real" site.

Unless you have made any modifications to how your site gets indexed, your main url (domain-name.com/directory) will get indexed.