Author does not provide a way for you to include Universal Naming Convention (UNC) path names for file locations. Using UNC paths is useful, especially if Spatial Servers are located on multiple machines. You can include UNC paths in a map configuration file, but you must manually add them.
<SHAPEWORKSPACE name="shp_ws-0" directory="\\mymachine\arcims" />
<IMAGEWORKSPACE directory="\\mymachine\myimages" name="jai_ws-0" />
Once you make changes using a UNC path, you can continue to open a map configuration file in Author and use it. The UNC path will not be deleted.