The upper set of colored cells is for the sudoku puzzle itself; the lower set of cells shows what digits are still available for use in the corresponding upper cell.  You may change the values in any of these upper or lower cells as you figure out the puzzle. 

You may use the large box in the upper right to easily import or export a puzzle.  For the import and export functions, a zero is used for empty cells.  You may use a comma (,) or period (.) as a separator, or skip using separators completely.