Bear in mind that the centre column has been designed chiefly to display the really "dynamic" content - stuff that changes a lot...
This is why the SIDE columns, HEADER and FOOTER are best used for content that remains fairly constant.
If you want to put the search facility into the centre column, you will have to re-code a large number of files. In addition, getting the search function to display in the same place will be a real challenge!
As you will want the search feature to always display - and to display in the same position - having it in the header or as a sidebox is usually the best option. Your visitors will see where it is, and will expect to find it in the same position, regardless of what content vis being shown in the centre column.
If you want the distinctions between the header, footer, side columns and centre columns to be "seamless" (in other words, they all look part of a common "page", then you must edit the CSS to remove borders, colour-bars, and other elements that make these divisions distinct.




