great
Then I would suggest one certificate with all your www.shopname.kwikkopy.com.au subdomians
I wrote an article about the DNS validators and how they can help automate things even further (not needing to manually add dns records). Tutorial - Certbot Cloudflare DNS with Apache Web Servers on Ubuntu 16.10
The second option is if you have bindings/vhosts for each of your sites in apache the apache plugin will do all the work of setting up the challenges for you. This also has the advantage that it will create the HTTPS bindings or update them for you for the new certificate (which may make things easier).
If you run certbot --apache --staging you can see how this works
When you are trying things out it is recomended that you use the staging server as it’s unlikely to hit a rate limit while you are configuring various aspects
Both the DNS authenticators and the apache installer are designed to make things easier (ACME is supposed to be fairly automated) and it’s worthwhile getting this right now as you have to do this every 3 months
Andrei