What is the name of the domain?
What is the issue you’re encountering
Wondering if I need Pro and use “Total TLS” or the Business Plan?
Was the site working with SSL prior to adding it to Cloudflare?
No
What is the current SSL/TLS setting?
Off
To make sure Cloudflare SSL covers your sub.sub.domain.com (like www.sub.domain.com or deeper), you’d have to purchase an add-on Advanced Certificate Manager at the Cloudflare dashboard for your zone, as follows at the article from below with more information in detail.
You don’t need to upgrade your Free plan type, you can pay such subscription for the ACM for as low as $10/month/zone to cover multi-leve sub-domains even on the Free plan.
Total TLS would become available to you for the zone within the ACM subscription being active, therefrom you could configure it as need.
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Ok cool… I have paid the $10/month for an advanced certificate but under hosts for the advanced certificate it says “*.mydomain.com.au, mydomain.com.au”
Sorry worried that it was only going to be one level? But the wildcard * is N layers deeps? eg ..mydomain.com.au is just going to work?
Once you hit the order button:
You’re asked to input and enter the sub.sub.domain.com and any other hostnames you’d want to cover with this SSL certificate:
You might not realise, therefrom you can enter sub.sub. and it’ll fill up the rest part of the domain name.
Once done, select the period and hit the Save button.
Wait for some minutes and check back.
You can enatle Certificate Transparency Monitoring to see once it’s been issued to receive a notification on your email which you can add up to.
Thanks… so I need to enter all the subdomains I want to support with a wildcard under each as required.
I’d give it a try with *.*.domain.com to cover all sub sub’s, however I haven’t tried yet.
In case if it would not accept wildcard *.* (apex followed by apex), then yes you’d have to enter each manually (up to 50 hosts per cert).
May I ask if you’re providing some kind of a SaaS service and need a couple of dozen of them to cover, or? 
yeh… it’s a product multi environments eg api.develop.mydomain.com etc etc
My opinion, go with ACM and see how it goes 
In such case you’d need more or would be looking for a further business expansion, there is an option SSL for SaaS to try out, however that’s an entire different field.
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