Sign in can either be accomplished by a link to the login page (link is typically found at the top), or with the Sign In module. The module allows direct entry of ID and password, but since it's a mojoPortal feature, it has to be placed within one of the CMS areas of a page (center, or left/right column).
Search is a bit different. The search box can be placed anywhere in the layout.master of your skin, and is styled with CSS, so the sky is (almost) the limit as far as where you can place it and how you can make it appear. For search box placement, see this thread with a helpful post by Joe Davis.
Jamie