I used some tape to experiment with various locations on my SP3. I would tape the pen loop to a spot, and use my SP3 for a couple of days in various configurations, with and without keyboard, portrait, landscape, etc. I put the pen loop/pen in just about every conceivable spot I could think of. In the end I found, for me, to put the loop/pen on the tablet, at the 'top' next to the rear facing camera (making sure it wouldn't cover any of the openings).
I found that location to be the most convent because I don't always have the keyboard attached all the time, when I use it in portrait mode the pen it out of the way under my left hand, because in portrait mode I put the Windows button at the top.
But try experimenting for yourself. Just don't peal off the backing on the loop until you find your ideal spot. The adhesive they put on the loop is really strong. If you peal off the loop, it won't stick again.