If you have the old 3ds you can use the system updater once you're in emunand *******Make sure you are in emunand before updating*******
If you have the N3ds then the highest fw you can have in emunand is 9.5. You can update using devmenu & a .cia of the firmware update (That is meant for the N3ds).
You can also update with .cias on the old 3ds as well (using an update meant for the o3ds), but it'd be easier to just use the system updater while in emunand.