There is really no difference EXCEPT when you mess something up. The box has 2, count them - 2, flash areas that you can boot from. In the beginning they (the nand flash areas) are (or should be) exactly the same. When you update, setup, or fidget with the box it saves those changes to whatever nand flash partition you booted from.
So, whatever nand you are using right now is fine when it's fine- but you can switch to the other nand when things get less than fine...