If the NANDs are linked then they will both change.
here is the simplest method -
Format emuNAND.
Boot into emuNAND
Go to system settings -> format (remove SD Card before format starts)
(or do this on sysNAND, I prefer my emuNAND is my main and my sysNAND is formatted)
Then if you make changes it should be separated, except for parental controls in my experience.
spankachu you are correct in the method, you should be unlinked.
How do you format emuNAND with mSD removed??!! emuNAND is on the mSD.