When users run a portal, they have either view-only access or customization access. If they have the ability to customize, all actions that they perform are saved unless a page is locked. This means that any time they move content around, the new positions of the content are saved. Any content added, hidden, or removed is saved as well.
New pages are saved, too. If the Portal Designer adds or removes pages or content, the user sees this, along with their customization each time that they load the portal. They lose their customization only if a page that they have customized is deleted by the Portal Designer.