There is only a single NIS Workspace file. This portion of the help that you have referenced:
"Browse to one of the following locations to open the XML file:
For 32-bit Windows operating systems�??<Install directory>\Program Files\ESRINautical\Desktop10.0
is\Schemas\Workspace
For 64-bit Windows operating systems�??<Install directory>\Program Files (x86)\ESRINautical\Desktop10.0
is\Schemas\Workspace"
Is simply referring to the path of the install location.
FYI, while ESRI has a variety of platforms that are supported, the Nautical Solution has a recommended subset that have been implemented and tested thoroughly.
So while 64-bit LINUX is supported, it has only been tested in a limited capacity.
Regards,
NancyZ