Hello Ernest and thank you for your support.
Then you can make multiple search instances, and each can actually use the index table engine. For example I see you have a search for archivo 2015 and 2016. So, on the index table panel just choose to index both blogs, then create the index.
On the search instance options, under the multisite options just choose the correct blog, and it's done. (you have this correctly)
You can do that to as many blogs as you want, and create as many search instances as you need.
RE: I was thinking about doing so, but is there a way of showing the subsite's category posts as a checkbox in the frontend?
The plugin cannot change the results page layout, it can only replace the results with the ones from the live results list, if the search is conducted through the ajax search pro search box. If I try to search via the 'Filtru Arhiva 2016' search box on the back-end, it takes me to the search results page, and I can see the correct results, linking to the 2016 archive. Is this not working on a specific page, because I tested it from the back-end? I could not find this box on any page on the site, that's why I tested on the back-end.
RE: that's cool. I think I've misinterpreted when I was reading the documentation.