Hello @andrewjs18,
Take a look to ./letsencrypt-auto --help webroot
and you will see two options to specify a webroot per domain/domains.
Example using -w ( --webroot-path ):
./letsencrypt-auto here_your_options -w /var/www/domain.tld -d domain.tld -d www.domain.tld -w /var/www/otherdomain.tld -d otherdomain.tld -d www.otherdomain.tld
Example using --webroot-map:
./letsencrypt-auto here_your_options --webroot-map '{"domain.tld,www.domain.tld":"/var/www/domain.tld", "otherdomain.tld,www.otherdomain.tld":"/var/www/otherdomain.tld"}'
Cheers,
sahsanu