Quill,
There are two ways that I fish stone fly nymphs and the manner is determined by how I am fishing.
If you are drifting down a river in a drift boat, then fish them down deep and on a dead drift, much in the manner that Joe Valencic suggested. Have that stonefly right at the bottom, because that is where the real stoneflies are. You can often fish then close to the shore since that is where they are crawling to in order to climb out. However, they live across the whole bottom of a river and often do get dislodged and drift free for a bit until they can grab onto something. While the fish will key in on the ones crawling to the bank, they will gladly take a stonefly nymph anywhere in the river. So, work the areas where you would expect to find trout like underwater ledges, and seams and obstructions like rocks. I use strike indicators to work this method.
If you are on foot and working the river from the bank then start fishing your stonefly nymph or even a black Woolly Bugger, upstream of you and slowly work your way upstream. Use short casts as line control and fly control is critical. You are casting right up against the bank allowing your fly to drift free back towards you. Slowly take in a little line and raise your rod as the fly approaches you, then cast back upstream right against the bank again. Work only the same side of the river or stream where you are, if you want to work the other side then cross over and work upstream from there. Naturally, if you see a good looking ledge or rock, it never hurts to cast upstream of that object a few times as well to see if you can entice a fish. Move upstream a couple of feet and start casting again. There is nothing on your line except the fly so keep good line control so you can see or feel the take.
Good luck and good fishing.
Larry ---sagefisher---
Organizations and clubs I belong to:
Fly Fishers International Life Member
FFI 1000 Stewards member
FFI Presidents Club
FFI Fly Tying Group Life Member
Washington State Council FFI
V.P. Membership
Alpine Fly Fishers Club
President & Newsletter Editor--The Dead Drift
North Idaho Fly Casters club