It's not as easy as you think; RapidLeech can't really work with sub-folders so even if you get your files extracted as sub-folders, they'll be useless unless you modify a lot of other files aswell.

Anyways, if you really want to extract using the full path within the archive, find this inside the extract() function:

PHP Code: 
$this->runit('e -ierr -o- -c- '.$password, '"'.$file.'" "'.$dest.'"', $jsoutid, $debug_id); 
...and replace it with:
PHP Code: 
$this->runit('x -ierr -o- -c- '.$password, '"'.$file.'" "'.$dest.'"', $jsoutid, $debug_id);