I feel that the search box that is always visable should be used to search current forums/threads instead of having a seperate search box you have to hunt for.
For example if you are in a forum the seach box says "search this forum..." or "search this thread..." and obviously you are able to change where it searches by selecting the location "Everywhere" or "This specific forum" or "this specific thread".
I don't know how hard this is to achieve from a coding stand point however, to me, it's a bit odd that there can be 2 search boxes that basically have the same functionality.
With Windows for example, if youa re int he control panel and use the search, it searches the control panel. If you search using the start button it searches for everything, if you are in your documents and search it searches your documents. Never do you end up with 2 search boxes on the same screen.