Domains and Website Builder

We currently show 2 domains, 1 ending in .com the other in .org. We should be .org. When I go to website manager, it automatically goes to .com, I don't see how to change it to .org, but when updating the site, it updates both .com and .org. So I am quite confused by that. Also, we are using Sitebuilder Plus. I see info that states we should change to Website Builder. If I click that, it directs me to start building a new page, that is also mobile friendly. It does show that by working on a new page, that the current will not be disrupted. Is all of that accurate, and do you suggest starting under Website Builder?