I have a multisite subfolder set up with 10 subfolders. They are all the same domain. I had to resort to an external site map generator.
My problem is I'm getting five the 600 visitors a day and Google webmaster tools recognizes on a good day about 90. This is mainly because it doesn't see the other sub-folders. Although it has indexed about 400 pages thanks to the external site map.
I wonder if I'm not missing something fundamental and how to set up sub-folders. I had started with yoast WP-SCO and and installed it on every sub-folder.
PS: there are many reasons for the multi site structure in this particular installation. If anybody's interested be happy to explain it. You can see it at http://www.INMRC.com