These seem like completely different questions to me.
Currently the Admin section doesn't have any feature allowing the layout to be customized. In the future I plan to do some work to improve the layout of the Admin section using some Ajax things like dojo but it is not my goal or intention to make the layout of the admin customizable per se. Maybe if I find any easy to use thing in dojo for draggable dockable panels I will provide for some arranging things, we shall see. I would consider adding an option that allows specifying a skin for the admin section separate from the main site skin but there is currently no such option and changing the skin doesn't really change the layout of the Admin features.
Your question is about showing and hiding pages in the menu depending on whether the user is logged in. mojoPortal has an Authenticated Users role that all users are automatically added to making it easy to create pages that are only visible when logged in by making them visble to "Authenticated Users" role.
We do not currently have a feature for hiding pages from authenticated users, only for hiding pages from unauthenticated users or from users not in the allowed roles. It would be easy enough to add an option in Page Settings for "Hide From Authenticated" so that we can support pages that go away after you login. I will look into doing that sometime soon.