Some people clip tie them to the frame, some to the rack. Others stand them up inside the panniers using tape to hold them against the back of the pannier (nearest the hub). Some people are lucky and have spare spoke holders already on the bike frame (usually on the left side). Others carry them in the trailer.
I've taped them inside & on the outside of the seat tube, and velcro'd/twist tied/tie wrapped them to various parts of my frame. Currently, mine are inside my seat tube because the spare spoke holder is interfered with by my kickstand.