This is the main window of JPEG Imager where you can add an image in order to edit it. On the left, bottom and right sides you can see 3 toolbars that contain image editing instruments 

The image effects that you can apply can be easily accessed by right clicking the image. You may adjust the Gamma, the Color balance, Levels, Tones or you can apply other effects and filters 

Here you can see a compared view between the source image and the output one. In the preview panel you can see how the Tones have been adjusted by modifying the Hue, Saturation and Luminosity 

The Preferences window only refers to the undo stack size and other file related settings like checking the compressed size or showing the filename in the taskbar