MODFLOW Versions and Storage Coefficient
MODFLOW96 and MODFLOW88 determine which storage coefficient to use based on layer type and comparing the head to the Top of the layer. For layer type 0 (confined), it always uses the storage coefficinet (S). For layer type 1 (unconfined in layer 1), it always uses specific yield (Sy). For layer types 2 and 3, if the head in a cell is above the top of the layer, then it uses S. If the head is below the top of the layer, it uses Sy. This is done on a cell-by-cell basis so that parts of the layer can be confined (S) and part unconfined (Sy).
MODFLOW2000 and MODFLOW2005 only have confined and unconfined layers, like type 0 and type 3 in MODFLOW96 but the principal is the same. However, these MODFLOW versions require you to enter specific storage (Ss). The storage coefficient in a confined layer is then computed for each cell by multiplying Ss by the layer thickness.
Groundwater Vistas does not compute Ss for you if you have S in the storage database. You need to enter the proper values based on the version of MODFLOW you are using. GV will, however, convert from Ss to S for MODFLOW96/88. There is a check-box under Model/MODFLOW/Package Options - BCF tab, that says the storage database contains specific storage (Ss). In this case, GV will multiply Ss by layer thickness for MODFLOW96 and MODFLOW88 BCF Package input.
Clear as mud?