Preferences

The PhotoTune preferences control many important aspects of the software. Preferences are persistent, like a switch and maintain their settings until you change them. You can access the Preferences from the Photoshop menu on a Mac OS X system or the Edit menu on a Windows system.

Apply PhotoTune to:
The Apply PhotoTune to options controls what layer information is sent to PhotoTune for processing. The options are a copy of the current layer or the current layer.

Option	When to Use
Copy of Current Layer: Creates a copy of the current layer and returns the results of PhotoTune to that layer, placed above the original target layer. This option will duplicate an existing layer mask.	Use this option if want to maintain your original layer with no changes to it. This is the default setting.
Current Layer: Applies the results of PhotoTune directly to the image layer itself.	Use this option if you are working on a 16-bit image or if you want to keep your image flattened. You can always undo PhotoTune if you don't like its results.

Preferences will take affect until the next time you open PhotoTune.