Hi wdrru.
This is a simple and yet difficult question to answer. What
you need to do is think carefully about what you are trying to
achieve and the ease with which you can do it. It sounds like you
will end up with a big help system. Will this be is a single RH
project? I suggest you split it up into logical chunks and merge
the relevant chunks with the larger "whole" help file. IMHO this
makes the management and operation of editing a help file easier.
You don't say how many topics you have but once your topics grow,
opening dialogs to add links, related topics, etc, take longer and
you may have to go away to make a cup of coffee and drink on
initially opening the project each morning. It's hard to put a
figure on this as it depends on how many other components such as
images, bookmarks and links are in the project.
As far as whether you should ship the "whole" or part help
file is down for you and your developers to agree on as it depends
on the user requirements, marketing, etc.