I have an addon domain which is a subdomain of my main domain, and I am trying to issue SSL certificates for addon domain non www and www, I have my A Host record set up, but am needing to know how to obtain the certs for the www and non www of addon domain which is forward and masked to the subdomain of the main domain. How do I set the A host records for addon domain domain2.com, if I set it to the server IP Address wont that disallow access from main domain domain1.com, I have certs installed for all subdomains of domain2.com but not www and non www
There is still a lot in your explanation that is unclear:
As for your questions:
That depends primarily on the operating system on your server and the validation method your decide to use (HTTP or DNS) to obtain the certs.
Adding DNS A records does not change the way a server operates. So, in short, no - it will only add more names that resolve to your IP and that you can serve content for from that IP.
You would need to add those records in the primary DNS zone for that domain.
I have domain2.com IP A Host record set to my server, but when I attempt to obtain certificates for domain2.com and www.domain2.com it says it obtained them and then does not show that the siites have SSL certification.