MiWorkplace includes the Open Source debugger from the JTOpen program. It is a wonderfully intuitive debugger and you can debug server jobs right from the GUI.
Start debug button in the context menu of the connection in the Remote Explorer, and the debugging session will be started.
Resources on the web
There are some good resources on the web about the IBM i System Debugger. Most notably from IBM itself at their developerworks section.
Other resources are