Milestones you add yourself now start private, as the standard milestones already did. The switch in the add and edit milestone dialogs is now Show on client dashboard, off by default: leave it off for a reminder to yourself, such as your own review before a submittal, and turn it on for the milestones your client should see. Nothing changes for milestones you've already added.
Everything else works as before. The Dashboard column on the permit page shows which milestones a client can see, with an eye icon to show or hide each one, bulk Show on dashboard for several at once, and Show … private milestones on the project page for a whole project. Milestone notes have always been private and still are, so they're the place for anything you'd rather a client didn't read.