Mapped Domains on Multisite SSL Lets Encrypt

I have Lets Encrypt working on my multisite installation. and are working and are all https.

The problem comes with mapped domains - I have several domains mapped and can't get it to work.

I've been reading extensively about this but seem to be missing out a vital step.

I've been looking to use certbot at the webroot and including -w /var/www/other to direct to the mapped domains but can't work out where they should be going. Which webroot should I be pointing to?

My server is Ubuntu 16.04 - PHP 7 - Apache