Your contractor may have some flexibility, but you'll have to show some too. You should ask for a written schedule, and then arrange regular weekly meetings with your contractor to review progress, update the schedule and discuss any other issues. Most homeowners give their contractor keys to the house for the duration of the job. Then discuss who will be given the combination to the lockbox. There are other security issues talk over as well.
Conscientious contractors make skillful use of plastic, plywood and shop vacuums.
They also sweep the job daily and do a more thorough cleaning at the end of each week. Still, you'll want to protect TVs, stereos, computers and other sensitive equipment. If anyone in the household is allergic to dust, let the contractor know about that up front. They should be written up as change orders. Make sure to go over the procedure before you have to use one.