Your code and assets for your application are organized as projects. Projects are basically containers or folders of related assets to create an app.
Projects allow you to group assets together in an IDE. You can manually create the same folder structure as a project created in the IDE to organize your code and assets so that edit and build your project using command-line tools.
Typically, the APIs provided in the BlackBerry 10 Native SDK are C libraries. Your projects can either be managed or makefile builds. Managed builds essentially require you to use QNX Momentics IDE while a makefile is more portable if you choose to develop outside of the QNX Momentics IDE.
You can use a template to create a project. There are various templates to start from depending on whether you want to begin with sample code or not. If you have a makefile-based project already, you can import the existing source code into a new empty project.