If you're going to be using egg patterns and stoneflies, your best bet is to use your favorite indicator type and set it so that the fly ticks bottom every so often. If you're not getting snagged up every so often, you're likely not in the strike zone. Set your weight (tungsten, shot, whatever you prefer 12-20" above the fly. As far as tippet goes, 3x or so is a good average, around 8 pounds, though you might find yourself having to go lighter based on the conditions. Personally I use fluorocarbon both for its buoyancy properties (it sinks more than nylon mono) and its visibility (closer refraction index to water/less visibility to fish). As far as where the fish are, that is going to depend on a number of factors, from when you arrive in the season to weather conditions to what has happened in the particular run you will be/are fishing. You're better off trying casts tight to the sides of rocks and just in front of them, as fish are less likely to be directly behind the rocks (though they often will be near them). However, try the pools just behind the riffle. As the water gets colder the fish will move back closer to the tailout if I'm not mistaken, but early in the season they should be closer to the head of the pool, unless they've been disturbed. Somewhere that gets pressure like the Salmon River can often see situations where the fish aren't where you would expect to find them because another angler either is or was standing in holding water. Don't forget to fish the inside seams, as often anglers are so caught up chunking casts to the far seams that the inside seams don't get attention. As a disclaimer, all of what I have typed here runs the risk of being entirely incorrect, but I hope it helps.
