Controlling the colors available in your templates

When you set set the runtime options for your template you will have the option of including either the generic colors palette and the document colors, or the document colors only, and a second option that will show all document colors defined, or only those that are actually used on each individual page.

To be included in the palette, each of your desired colors must be defined as a swatch in your document. If there are other colors (default colors that are included by InDesign, for example), the you don't want to include, delete them before you upload your template.