The CIS admin tool will only administer settings related to the CIS part of Capture CIS, so it will let you globally manage the following information. I've put comment in after each section
[Part Management] - this tells the location of the DataBase Configuration file for CIS (which holds the actual CIS configuration and requires the correct ODBC setup, which means the ODBC driver name must match the one used in the dbc file)
[Footprint Viewer Type] - specifies the footprint viewer type in CIS, choice is Layout or Allegro
[Allegro Footprints] - this specificies the directory where CIS can look for footprints to display during place database part operations
[Part Library Directories] - this is the path to where the schematic symbols are for doing place database part operations, so if a schematic symbol for a part is not found in one of the libraries in this section it will not be shown in the place database part dialog and you won't be able to place it.
[CIS Browse Directories] - this is the locations for datasheets (pdfs, docx, xlsx etc.) so if you have a datasheet in your database CIS will look in these paths for the datasheet when you click it inside the place/view/link database part window.
You will not be able to handle other Capture.ini settings through this tool.
I hope this help?