System Preferences > Network (henceforth "Net Prefs") allows you to have more than one of what they confusingly call "services" for each interface. For each additional manual IPv6 address you want to define, you need to add an additional Net Prefs "service" for the relevant network interface.
When you first go to Net Prefs, the prominent list of interfaces is technically, by Net Prefs' terminology, a list of "services". Hit the "+" button at the bottom of the list to add a new "service" for an interface. You'll be asked which interface the new "service" applies to, and you'll be asked for a name for that "service". So if you want to add a second IPv6 address to your built-in Ethernet, select "Ethernet" and name it "Ethernet 2nd IPv6 addr" or something. Then go to the IPv6 settings for this newly-created "service" and configure it for your secondary IPv6 address. Repeat until you've made a separate Ethernet "service" for each IPv6 address you wanted to manually assign.