I'm afraid I have not fully understand your question. Please note if you generate a SSL certificate for
www.domainA.com, and a while after you create a new site for
www.domainB.com, you will need to generate a new certificate for all the 4 domains:
domainA.com, www.domainA.com, domainB.com, www.domainB.com
Did I answer your question? If not, could you please elaborate your question a bit? What did you fix using the Really Simply SSL plugin?