One of the key things for your Mathematica project is to run and test its code. The Workbench lets you do this in a variety of ways.
The simplest way to use the code in your project is to open a notebook document from within it. When you do this, the source paths are all added to the Mathematica $Path so that you can immediately start to work with your application.
Note that if your project uses code from other projects, set up with project references, these are also added to the Mathematica $Path.
If you want to debug the code in your application you should do a debug launch. Then you will be able to set breakpoints and rectify problems in its execution.
In order to verify the operation of your application, you can easily develop and execute a set of tests written with the MUnit unit tester.