Bought a 2016 Cannondale Quick Speed 1. Love the bike but I am not sure if the seat is in the right position. I am only 5' 8" tall, but I am all upper torso. My pants length is between 29 and 30. I think I have the seat at the right height but when I am seated, I feel like my head might be too far at or past the handle bar. Where should a riders head be in relationship to the handlebar when riding a hybrid bike?

I like the setback .. from pushing the saddle back ,

You may want seek out a longer stem , to move the handle bar further forward.

I have a line of sight straight thru the steering axis when i look down ..

another popular thing is to have the handlebar visually hiding the hub.

I would be very surprised if any of those 'fitting maxims' developed by, and for, road racing cyclists held true for less athletic riding done on MTB or Hybrid designs. "Longer stem"? On a road racer a longer stem stretches you 'out'. On a hybrid a longer stem stretches you 'up'. Proper seat height for any bike is the one that allows the seated cyclist to pedal the bike with the heels on the pedals. Unless you have bigger, or less than, 85th percentile foot size this should get you very close to an optimum saddle height. On the road racer the next step is to fine tune reach adjustment. On a hybrid (assuming it was the correct size to begin with) you are done purchasing components. If you cannot abide by the resulting position reached by adjusting the stem height you are probably over-thinking "fit".