If you’re adding a completely new document (as opposed to modifying an existing one), then you should create a new source directory for that document under <ARTISYNTH_HOME>/doc, and place the relevant .tex files there.
You should also create a Makefile in the new directory. This is most easily done by copying an existing Makefile from a similar document, and replacing the names of the source files. Note that many of the commands and variables are predefined in the file Makedefs, included from <ARTISYNTH_HOME>/doc.
You should also update the Makefile in <ARTISYNTH_HOME>/doc, so that it is aware of the new document subdirectory. Most likely this will just require adding the name of the new source directory to the variable SUBDIRS.
Adding a new document will also require updating the configuration for the InfoCenter (Section 6), so that the InfoCenter knows about it and can add it to its table of contents. See the section “Adding a New Document” in the file
The ArtiSynth website provides links to the various manuals and guides (including PDF, HTML, and InfoCenter). These should be updated to provide links to any new documentation, particularly on the main documentation page at www.artisynth.org/doc.