The Swiftype WordPress plugin does not fully support WordPress Multisite at this time. It can be used with WordPress Multisite, but you will need to create a unique search engine for each sub-site. Due to this incompatibility, federated search across all sub-sites is not currently possible.
It’s on our roadmap to add support for WordPress Multisite, but we are not sure when this will be available.
As an alternative approach, you can use our web crawler to create a single search engine that indexes multiple domains/sub-sites. You could then use our JavaScript embed code to take over WordPress’s standard search, or even write your own search experience using our jQuery client or Web Components libraries.