The placement of the left and rights side blocks are pretty much determined by the theme's template files (leftblocks.thtml, rightblocks.thtml, which are pulled in at the end of header.thtml and the beginning of footer.thtml, respectively). So you could probably do something there by rearranging table rows and columns.
The standard middle section (stories and center blocks), however, is produced by index.php. To make any significant changes there, you would have to hack that file.
I assume you already found the
theme documentation?
HTH
bye, Dirk