SSL on Multisite with subdomains and using SNI with letsencrypt/certbot

I have a multisite and am trying to use SNI to set up SSL for each individual subdomain. I was thinking of purchasing a wildcard SSL but then I found letsencrypt with certbot. Everything seems like it should be easy enough but what I run into is that every plugin to enable SSL on wordpress wants to redirect the subdomains to the main domain from http. I can not figure out how to not have this happen.

Also when I put in a subdomain site, it always wants to use the original SSL of the main domain even though I have set up different VirtualHosts on port 443 for the subdomains that point to the correct certificate files.

I feel like I am just at the edge of understanding all of this and if I just need to add in a separate SSL with SNI for each domain/subdomain and change some code in my .htaccess and 000_default.conf (apache2) files that would be fine for now.

Someday I want to set up some prosites managed hosting but for now I am just creating the different sites myself for clients.

I have been pouring through forums, blog posts, etc. etc. all day. There seems to be enough information out there but unfortunately with my limited experience I am unable to put it all together correctly.

Thanks for any help offered!