It depends! If you want to save counter space I would put it below. But for me, when I put the coffee on top, it wouldn't fit under so I could open the coffee maker. So now it's beside it but I put other things on top!
I suppose it would be up to you, but to save counter space I keep mine under my Keurig. I have to pull it forward to use it so that the top doesn't hit the cabinet when it opens but it's definitely worth it.
I keep mine stored under the machine. The only problem is sometimes it will hit my cabinet because the machine is too high. But I just moved it a little forward. I love mine it's a sleek way to hide your Kcups.