I can't comment on your local pricing as I'm a couple thousand miles away, but I can tell you that while the prices seem reasonable, there isn't enough information for a meaningful answer. Roof pitch (steep can be anywhere from 7/12 up to 15/12 or more), valleys, hips, height above grade (number of floors), number or existing layers of shingles, etc. will affect the price quite substantially.
Not familiar with Atlas, but upgrading to a dimensional shingle is always a good idea in my book.
Flashings can be a big bite, make sure that you have adequately addressed that before signing anything.
Whatever you are planning on doing, I suggest you do it as soon as possible. There is a large black hole on the Gulf coast that will be sucking down labor and materials at an amazing rate.
R