Sorry for not being detailed, im on o3ds. So from what you're saying, i should boot to emunand (with rxtools) and update from system settings yeah?
Yes, update using Other Settings -> Software Update when in emunand (and without exiting). This is how I've been doing it on my own and on friends. We use linked SYSNAND and EMUNAND. I read somewhere, if these are linked and you use sysupdater, you end up updating both.