To change a thread palette / a thread color:

Change the design's color palette with the menu item "Design" > "Thread File". By default StitchBuddy will adjust every new color to match the current palette.
If you don't want this color matching, select "Individual Colors" and every color stays exactly as selected. A ".thread" file will be written at the same location when saving the design. Because individual colors lack a specific name, only their RGB values will be shown.
Choose "Discard Thread File" to use original colors of a design: The internal color palette (JEF, JEF+, JPX, PES, PEC), RGB colors (VP3, PCS) or no colors at all (EXP, DST, KSM). The current ".thread" file which holds extended color information is deleted when saving the design. As this action effects other embroideries with the same name (there's only only one ".threads" file for all these designs) a confirmation is required, which can be dismissed for the future. To reactivate the warnings check the corresponding option in StitchBuddy's preferences.
Select any other menu item and selected colors will be adjusted to the most similars of the given palette. A ".thread" file will be written at the same location when saving the design.

To change a single thread color, you can simply click in a corresponding area of the design. All other colors will be displayed in grayscales and a color picker is shown for the selected color ("Enhanced Color Selection"). You can achieve the same efect by clicking on a color name in the thread list. Revert the display to show all colors by clicking again on the selected color / color name or an empty part of the design. This enhanced color selection can be disabled in the preferences, leaving the color box the only possibility to activate a color picker.

The color picker of Mac OS X provides several ways to choose a new color: With the color wheel you can click directly on the desired color, on the RGB panel you can specify the red/green/blue values of a color, or you can use color lists to pick from. Some major color lists of embroidery threads are provided with StitchBuddy, but please be aware that the displayed color of a thread may vary between different applications and nature. These color lists support searching and it is even possible to create your own list with your favourite colors. The most convenient way is to use the same color list as the design's palette, but that's not mandatory.

To change another color it is not required to close the color picker: You can just click on the next color well, a color name or a corresponding part of the design to select the next color.