JonD, I am happy you chose Mail In A Box to self host your mail server.
Like you, I too have my domains registered on Cloudflare. I would like to advice you that Cloudflare allows you to delegate a sub domain to name servers hosted by Mail In A Box using the “NS” record.
Let me say my domain name is “EXAMPLE.COM” and so, I create “qwerty.example.com” in CloudFlare dashboard and add two “NS” records and point them to “ns1.box.qwerty.example.com” and “ns2.box.qwerty.example.com”.
Now, I make a stub “ns1.box.qwerty.example.com” with an A and AAAA record to the appropriate IP address. Likewise for “ns2.box.qwerty.example.com”.
Now, I run the Mail In A Box setup and my box is setup and I will have a personal email address me@qwerty.example.com.
I am using sub domain “qwerty.example.com” and if I want to allow mail for the root domain, “example.com”, I can setup Email forwarding with CloudFlare to forward all email to @example.com to the Mail In A Box account, me@qwerty.example.com.
If you have more than one domain in CloudFlare just create a sub domain name for each domain that you want to setup Mail In A Box on and delegate it to two name servers that will host your Mail In A Box.
This works not only on CloudFlare DNS but also NameCheap DNS. Both registrars allow free email forwarding.
Its very easy 
JonD, I hope you can understand but if you still do not please tell me what you do not understand so I can try to help you.