There's no reason to lose your saves when switching to Atmosphere. I highly recommend using a hidden partition for emuMMC rather than file-based. Your best bet may be to use JKSV to backup all your saves, and then make a fresh, partition-based emuMMC. Then restore your saves.
Every atmosphere release has the newest payload (same with hekate). Download and use that (for the case you don't have the fusee.bin). And btw. every changelog says, that you have to update the fusee.bin