There are many places in the root filesystem where you can put your own application, depending on the number and types of components it has. Usually, it is preferable to follow the FHS's guidelines to place your software.
If your application consists of a relatively small number of binaries, placing them in /bin is probably the best choice. This is the actual installation path used for the control daemon in Chapter 4.
If your application consists of a complex set of binaries, and possibly datafiles, consider adding an entry in the root filesystem for your project. You may either call this new directory project or name it after your own project. In the case of my control module, this directory could be control-module.
The custom directory can contain a hierarchy of its own that you can customize to best suit your needs. You may have to set the PATH environment variable on your target to include the custom directory if your binaries are placed there.
Note that the addition of a custom entry in the root filesystem is contrary to the FHS. This is a minor violation to the standard, however, since your filesystem is custom built for your target and is unlikely to become a distribution of its own.