There are a number of useful articles written about Kryptos, that are very interesting to the amateur cryptographer such as myself - your best bet for this particular question is probably Frank Corr's post on derkeiler.
It uses two grids of dimensions 21 x
16 and 28 x 12. The plaintext ends up
being written into the first grid by
row, starting at the top row, and
removed by column, starting with the
last column and moving backward. It is
then run through the second grid in
the same way.
It is much easier to understand when described like that.