Debugging is one of the key features of the Wolfram Workbench.
To start a debugging session, you would typically
Mathematica in a debug mode and ensure that
all the files that you wanted to work with were
loaded. More details are found in the launching
section. However, a quick summary is to select a .nb file, right-click,
and choose Debug As > Mathematica, as shown below.
An important utility for debugging is the Debug perspective. The perspectives section gives some general details about perspectives. When the Workbench is in the Debug perspective, a number of views and tools that are useful for debugging become visible. When you hit a breakpoint, the Workbench will automatically switch into the Debug perspective.