If the source code is in directory A, the output binaries are in directory B, and the extra includes are in directory C, all of the directories have a common root, D (i.e. D/x/y/z/A, D/x/C, and D/w/C).
To create a project by itself, with it's metadata located in another location (and you also want to share it if possible):
You can continue to create a make project using the C or C++ wizard. For instructions about how to create this type of project, see Creating a make project.
If you're creating an application from scratch, you'll probably want to create a QNX C Project or QNX C++ Project, which relies on the QNX recursive Makefile hierarchy to support multiple CPU targets. For more information about the QNX recursive Makefile hierarchy, see the Conventions for Recursive Makefiles and Directories chapter in the Neutrino Programmer's Guide.
Use the New Project wizard whenever you want to create a new project in the IDE.