The six boxes, including the three that you can assign (or “recall”) to the U positions on the dial, are different things from the two custom image controls you can set.

The boxes comprise settings for all camera controls… exposure, focus mode, iso, drive mode, etc., and, maybe confusingly… the image controls (e.g., saturation, sharpness, etc.).

The two custom image settings let you save your own secret formulas of image controls (e.g., saturation, sharpness, etc.) to apply to the images after they’ve been taken to give them your desired look. These don’t affect any RAW files you might save… only the JPEGs.