Kapishth Indra in Siddhachakra Vidhan likely refers to the step called Indra Pratistha (Indra installation) that begins the Siddhachakra Mahamandal Vidhan. In this step, the Indra deity is invoked/installed at the start of the ritual to invite auspiciousness and proper sanctity for the worship. The exact wording and sequence can vary between Digambar and Śvetāmbara traditions, but the core idea remains: establishing a guardian deity to bless the ritual and aid spiritual focus during the Siddhachakra/Navapad worship. You can read more about Siddhachakra Vidhan and its components here and about Siddhachakra/Navapad worship here