Import one of the provided CodeWarrior examples into your Workspace so you have the proper connections.
Click on the Flash Programmer icon () to open the Flash File to Target dialog:
Select the proper connection by clicking the Browse… button and locating your file (typically with .S19, .OUT or .AFX extension). Click on Erase and Program and wait until it the task finishes:
Once finished, you might need to manually reset the target to get the application running.