Multisite support

I installed the plugin because I saw that it was compatible with WordPress Multisite, but I couldn’t find any documentation on how the plugin works with WordPress Multisite. Can someone help me?
I have WordPress Multisite with subdirectories. So I have mydomain.com, mydomain.com/blog, mydomain.com/store. I would like to understand how I should proceed about this. Do I have to request an SSL certificate for each subdirectory? Should I add the domain or subdirectory under “Domain Name”?
I hope this question is helpful to all the other people I could see who are having the same problem and this plugin can be a solution for everyone.