In theory the only difference is the added volume of the board. I agree that the stand up is easier to remove what you want and gives you a bit more of the surface of the fabric to look at when stored. The best wasy is what works for you and your storage space. Fold in the manner that best fits the space you have.
I also wrap around my 6" ruler so if I forget to mark and can estimate the length of the piece of fabric by counting the number of layers.