Letsencrypt and NGINX for subdomains

I have a multisite on a serverpilot nginx/apache setup and am trying to install letsencrypt SSL certs for subdomains.

Its fine for the main domain but when I try using webroot even though I specify the webroot path to my multisite wordpress root the authentication expects a path to .well-known etc to be in a root of the subdomain.

so the test for bell-computing.com/.well-known/acme-challenge (from the webroot of /srv/users/serverpilot/apps/myappname/public/.well-known/acme-challenge.

but the authentication tries and fails to authenticate for staging.bell-computing.com/.well-known/acme-challenge

I have always had mapped domains onto subdomains before and that works fine but I not for straightforward subdomains.

The Letsencrypt experts in their forum are trying but don’t really know what wordpress is doing in terms of the subdomains. Folders might work but thats now aht I want to use.