Leaving system settings will let it boot back to system nand.
Here is what you should do.
When you first boot your 3DS, without using Emunand, create a few folders to show you are in sysnand, like this:
Now install whatever, enter Emunand and insert your flashcart.
Now rename those folders:
(ignore the fact that my games don't appear on sysnand)
Now to be sure, power off and on.
What folders do you see?
If you see the sys folder again, you know which mode you are in.
and when you emunand, you see the emu folders, you know what mode you are in
Once you can confirm that the folder method is accurate,
you won't need to enter and exit to check again.