If you need to install something in sysNAND while in Gateway mode, then you need to remove the sd card.You don't even need to do that (and I personally wouldn't recommend it either). All you need to do is turn the system off in emunand and turn it back on. Simple as that.
Reason why you might want to be in both sysNAND and Gateway mode is to install things like cearp's DS flashcard time machine or CN (Since you sysNAND is 9.2 or below)