Well, the high-bar position generally is best for building athleticism and has better carry over to other lifts, but the low-bar position will allow just about anyone who uses it to immediately squat more weight. My thoughts are that if you're training for anything other than powerlifting, use the high-bar squat. I even think it's good for powerlifters to do the majority of their training high-bar and then move the bar down lower as specific meets get closer. I think the majority of people end up using low-bar all the time as an ego thing.
The high-bar position is usually used to squat with an upright torso and the low-bar position is used with more forward bend. If you were squatting high-bar and ending up hunched over trying to good morning the weight up, then you either have a flexibility/mobility issue or you have a muscular weakness. My guess is that you have a stronger posterior chain but have weaker quads. Since high-bar squatting is more demanding on the quads, you were probably trying to find a way to incorporate more of your posterior chain into the movement. You could start front squatting to build your quads up and try out high-bar again, or just stick with low-bar if you're happy with it.