Explanation
GIS is used to create a computerized layer cake of spatial information about an area, and each layer represents a single spatial attribute. The layers are all entered with the same coordinate system so that they are georeferenced. The different layers can be of things like "roads, streams, soils, elevation, etc. Information in the form of points (such as archaeological sites), lines (such as roads or steams), or polygons (such as a soils or a geology map.)" (GIS and Remote Sensing for Archaeology)
Uses in Archaeology
Analysis of the mapped areas is much easier with the GIS system than with traditional paper mapping. Coincidence tabulation between layers and spatial modeling of the layers can be done much more easily. The location of sites can also be predicted using the GIS system by using information about known sites and then looking for areas that have matching characteristics.
Link
http://www.esri.com/industries/archaeology/index.html
Resource