I put my bottle cage on the stem rise but at the side, slightly forwards so the bottle sits just behind the bars. This way, the back of the bottle is in front of the stem riser so doesn't interfere with my knees (might not be the case if you had a very short stem - mine is 140mm so loads of room for a bottle)
I also tried it behind the saddle, but the bottles kept jumping out when I rode fast over bumps (unavoidable on my journeys). After losing 3 bottles I gave up on the seatpost mount.