we are getting to the stage of needing to set up our SSL certificate/certificates and would like clarification on how to go about this....

Our projected structure will be sharMasterSubdomains mostly with parked / alias domains for each subdomain

master.domain.com (our Main site)

subdomain1.domain.com with parked domain xxx.com for a client.

What sort of SSL Cert do we need to buy, and for which domain?

All depends for which domain or subdomain you need a certificate.

If you expect just have subdomain certificate, it is possible to buy wildcard subdomain certificate.

If you want to have certificate for differnt domains names, you need to buy a solution for multi-domain certificate.

The constrain is that WHM/cPanel can only have 1 certificate per cPanel account.
Therefore, the certificate must be valid for all the domains and subdomains for which you expect to use the certificate.