If I'm fishing water where I need to get all the way down I like to use a heavy stonefly and then trail a smaller nymph behind it. As far as knowing when you are within an inch of the bottom, it is a feel/guessing game that only comes with experience. It will depend on depth, water flow, etc. The one thing I can say is if you think your not getting down, increase you leader/tippet or add split shot and then if you start hanging up, you're to low. You don't really want to bounce it along the bottom like steelhead; you want it floating just above the bottom. Line control (mendind, etc.) is very, very important when nymphing and a lot of people overlook that. A strike indicator will help you with that. You don't want your line dragging your flies; instead you want them to drift with the current and a strike indicator will help you visualize that. Experience is the key to being successful at nymphing because you never know exactly where your flies are or what they are doing.
When I first started nymphing I would get so frustated because my buddy, who had more experience than me, would always outfish me and pick-my-pocket all the time. After time on the water and learning to control my line, my hookup rate increased dramatically.