Hi Ray,
The Repository module's display is controlled by a 'template' which is made up of a series of .HTML and .XML files. If the template you are using does not have the Search textbox and button in the header area, you can add it by opening the HEADER.HTML file in the folder of the template you are using.

For example, if you are using the 'nifty' template. Open the HEADER.HTML file in the /DesktopModules/Repository/Templates/Nifty folder ( the folder is named the same as the template name ). Decide where in the header you want the search box and button and add a [SEARCH] tah.  Look on the Project web page here at dotnetnuke.com and download the Module Documentation. Check out the Tag reference in the templates section for more information on customizing the look and feel of the search text box and the button.

With the current version, all Repository files are stored in the same folder. In a future release, the Repository module will use the new core URL/Upload control that will allow you total freedom over where to store your files ( including in the database if you wish )