You can update the o3DS emunand by using system settings, or sysupdater. To update the n3DS you have to use sysupdater, because system settings update it to the latest version (?). And yes, you will keep the exploits installed (provided you did it correctly). If you try to install cia files using sysNAND FBI it won't show up in emuNAND, you have to do everything in emuNAND.