On bolt guns I still hold the belief that the scope has the lowest potential aiming error when mounted as close to the bore as possible. This usually works best with most bolt gun stocks.
This rule does NOT work on AR type rifles, where the stock is going to be higher. This becomes a personal preference. Most prefer having the scope with its centerline about 1.4" to no more than 1.5" above the top of the rail. Many prefer it a bit lower, down in the 1.3" range. No hard and fast rule, but you want to get a good cheek weld while still trying to minimize sighting error at longer ranges.
I believe in scope bubble levels. When shooting slow fire at bench they work great. But, you may not always have time to use a scope level, or have the best light to see one, especially when hunting or in certain tactical situations.