Before you go and dissect your carefully crafted 500 page project into multiple projects please take a few moments to run through this tutorial so that you understand the concept completely first.
In this scenario we have a holiday company who want to showcase their specialized holiday destinations which are categorized as "Cheap and Cheerful" and "Ghastly Expensive". They want most of their clients to see the "Cheap and Cheerful" destinations but only some of their clients will want to see both and some will want to only see the "Ghastly Expensive" options. So they create two projects as follows:-
Master Project
Slave Project
Merge the Two!
Now let's go back to the Master Project and add in our Slave Project:

Possible Problems with Merging
The current version of Microsoft HtmlHelp v1.4 has some bugs in Merging. We advise that you place your Merge Contents at the first level of the tree in Fast-Help, but you will notice that it is indented below the last entry in your Master Project. This is a bug. If you try to place your Merged Contents at any other level it will act erratically.
Another issue is spaces in file names, merging does not like it, so please name your Slave Project compiled files without spaces.