When you set the runtime options for your template you will have the option of including either the generic colours palette and the document colours, or the document colours only, and a second option that will show all document colours defined, or only those that are actually used on each individual page.
To be included in the palette, each of your desired colours must be defined as a swatch in your document. If there are other colours (default colours that are included by InDesign, for example) that you don't want to include, delete them before you upload your template.
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