Yep, pretty much, you just re-inject the payload. Remember that if you updated Hekate, you also want to update the payload, although it's not strictly enforced in the case of Hekate, since the older payload will detect if a new version is installed on the SD card and boot it instead.
Thanks again for your help.
Question about updating Atmosphere--is it possible to do so offline, i.e. by overwriting the existing atmosphere on the SD card?