The historical archaeologists at the Minnesota Historical Society
excavate by stratigraphic levels (soil change).  However, I believe that
most of the archaeologists in our department who were trained in
precontact archaeology excavate in arbitrary levels, except for
features.
 
Robert Clouse, head of our department, has taught historical archaeology
field schools for several years using stratigraphic methods.  Individual
strata are each given a "locus number" and the relationships between
loci are determined as excavation proceeds.
 
Our recording forms contain a section for recording "over/under"
relationships of strata.  We can then plug these "locus numbers"
(sometimes called contexts) into the Bonn Archaeological Statistics
Package Harris Matrix software and come up with a great Harris Matrix.
I recently received a trial version of Arch-E from the
Max-Planck-Institut but I haven't tried it out yet.
 
Elizabeth Knudson Steiner
Archaeology Department
Minnesota Historical Society
612.726.1171