The bookmark vault allows you to store your favorite sites, and is completely hidden until you unlock your vaults with your password.
After unlocking your vaults, tap the Bookmark Vault button in the sliding menu.
After unlocking your vaults, tap the Add to Bookmark Vault button in the sliding menu. In newer versions this appears as a + next to the Bookmark Vault.
Long press on a bookmark/folder to enter selection mode, then tap on the bookmarks/folders you wish to manage. You can: