Very confused about this. This seems like an ass-backwards way to install CIA's to sysNAND which is never advisable. Simple way is to copy CIA's to ONE SD card, run exploit, don't format emuNAND, run GW mode, install CIA's, format emuNAND. Then emuNAND will match your sysNAND with the CIA's you installed saving you a lot of time. Still not advisable but having two cards is pretty pointless for this process imo (I do have a second SD for my "legit" emuNAND and primary with my third-party site CIAs).
flashcardtimewarp.cia needs to be installed on sysNAND to work properly