If you only need one SSL, or no SSL at all, then the Magento MultiStore method does not matter. If you are going to have multiple SSLs, then the method matters.2
If you only want to have one IP address (that's already included with your SIP account), then you would need to use the Pointer Domain method combined with either a Wildcard or MultiDomain SSL.3
If you would rather not use a Wildcard or MultiDomain SSL, and would rather have individual SSLs for each site, then you would need to use the Secondary Domain method and have multiple IP addresses.4
You would also need to use the Secondary Domain method (with multiple IP addresses) if you intend to setup email addresses for these additional Store(s)/Domain(s).