You can "merge" additional Help+Manual projects ("modules") into your current project by inserting them in your Table of Contents, in the same way as inserting a new topic. This also makes it possible to use conditional output include options on entire modules in the same way as on individual topics.
Modules are inserted in the TOC in the same way as topics, so you can apply include options to entire modules in the same way as to topics. A module include option can include or exclude an entire project with its entire directory tree, all its chapters, sub-chapters and topics and all its invisible topics as well. If the module also has child modules a single module include option will include or exclude the module with all its children.
Modules can also have their own include options in all the chapters and topics in the module. These will also be evaluated and applied when you publish the entire modular project.
See Working with Modular Help Systems for details on creating and using modular projects.