Although you can specify paths to catalogs located anywhere on your local system, if you are using specializations, you need to create your own XML catalog for each, and put that catalog where your catalog key says it is; that can be a subdirectory of its own under the DTDs. In the DITA2Go distribution, the catalogs are located with other DTDs.
DITA2Go does not have any requirements related to specialization. If you specialize the DTDs, DITA2Go reads your new DTDs and just works. For a tutorial on specialization, see:
http://xiruss.org/tutorials/dita-specialization/
If you have already installed the DITA For Publishers plug-in for the DITA Open Toolkit, as an alternative to the d4pubs key defined in \common\system\config\omsys.ini, you can do the following: