As stated, typical AR mounts set the center of the scope at 1.5" above the stock. This replicates the factory iron sight settings. You may find a little more or less is comfortable, depending on how you like your cheek weld and the scope you use. Going lower than 1.5" can make for fairly uncomfortable prone shooting, but again this is a generality.
With regard to the eye relief, that will depend on where you like to mount the stock (Some guys mount the stock so that their nose is touching the charging handle - I like it where I'm a couple inches back) and what the eye relief of the scope is. Generally, with longish eye relief, you'll likely want to install the scope fairly far forward.
The best thing to do is loosely install your set up, and try it in all positions you will be using. Hold the positions for a couple of minutes to see if the set up causes you any strain.
I'm sure most know this basic exercise, but for those that don't:
-get into a position where you are centrally & comfortably aiming at a target, and where your breathing only shows a vertical transition between target and sights. (there should be no horizontal movement, as this indicates straining to stay centered).
- get into your breathing routine and adjust your vertical slightly where you're on target at the exhale.
-continue with your breathing and close your eyes for three reps.
- on your third exhale, open your eyes to see where you're sights are in relation to your target.
- With a comfortable position, you will be on target or very close - if you're straining, it will be a different story.
