The only important thing, when working on a project in the Bench environment, is to start the IDE or text editor through its Launcher, and to call command line tools from a Bench Shell.
When working with an IDE or a full-featured text editor, start it via
its Launcher in the Bench Dashboard or its shortcut in the launchers
directory. Then open your project from within the IDE or text editor.
This way, the process of the IDE or editor has the Bench apps on the PATH.
When working on the command line, just open a Bench Shell from
the Bench Dashboard or via its shortcut in the launchers directory.
Change the current directory to your project, which mostly is a sub-directory
in the projects directory, and use the command line tools you like.
If you miss a command line tool, checkout the app list, maybe it is allready
listed and you can just activate it.
You can find a more detailed description of working in a project in the tutorial Working in a Project.