We are having two domains. One is example.com(B2C/B2B Customer based site) and another one is My.example.com(internal employee purpose).
1) example.com - Already implemented with analytics with third party cookies.
2) my.example.com - we are going to do fresh implementation. Plan to get CNAME certification from clientcare.
My question is > Our plan to implement CNAME process for my.example.com alone for now. In future, if we ask for example.com, will it be a separate then? Can we ask them to provide one certificate for both the websites.
Note: my.example.com implement process on the same organization analytics account which we have used for example.com.
As per your example, my.example.com seems to be a subdomain of example.com so Adobe can create one FPC setup for example.com which can be used for both example.com and my.example.com. You can implement that for my.example.com now and later can use the same for example.com.
If B2B/B2C and internal sites are different domains(like abc.com and xyz.com) all together than Adobe would need to create 2 different FPC setups(one for each domain) and would require different SSL certificates.