Now, can anyone tell me how database A and database B can have the same content, yet if I delete database A my site goes down? I was under the impression that domain A linked to domain A databases only, etc.
That all depends on how you have them set up. You can have one database for multiple sites and accounts, or you can have separate databases for each site. You can also have all of the databases in one single account and connecto to them from any other outside account.