If I want to use a command token on a secondary strategic action, do I send it back to reinforcements?

Yes.

Thanks, it probably says this in the book somewhere, I just couldn't find it.

Every piece of plastic or cardboard that you have (either plastic colored figures, or cardboard with your race on it), and that isn't in play (on the map or on your racesheet, including the CC pools) is considered to be in your reinforcements.