During a project, it's best to stay out of the way and let your contractor do their work. But that doesn't mean you shouldn't monitor progress and speak up if something doesn't seem right.
When you do have concerns or questions, it's best to voice them to the contractor or project supervisor. The crew may just be acting on their orders and not be able to answer your questions. Also, peppering them with questions could keep them from finishing your job on time.
On the other hand, if you see something happening that you think is really wrong, such as a double hung window being placed where you agreed a casement window would go, stop the work immediately. Your contractor will appreciate your spotting the error and saving them the extra cost of removing the window and replacing it with the right one.