I have four colors that I use all the time. I have not figured out how to keep them as permanent swatches in InDesign. However they will stay in my CC Libraries>My Library>Colors. I cannot figure out how to either keep these colors as swatches that are included when I start InDesign or how to import the colors into a new document. The "Set Color" option does not work half of the time from CC Libraries>My Library>Colors box.
Add them, when no document is open. This will affect only new documents.