The application involves at least a hundred questions relating to the applicant's reaction to various customer service and food handling related situations. These questions are designed to give the company a score for each applicant, relating to things such as the applicant's potential truthfulness, their aptitude, and their emotional/stress handling level. Generally it's better to answer these honestly rather than trying to go for the "best" answer. This relates to the truthfulness rating.
If the applicant is approved, the management will call to set up an interview in-store. This generally takes place in the dining room area, with one or two managers. There is a script to follow for the interview, but many managers will simply ask whatever questions they think are best. There will generally be two interviews, often on the same day, so that each interviewing manager can give independent feedback to the other, then arriving at a decision.
If they decide to hire the interviewee, the interviewee will discuss starting pay, position, and starting date with the general manager, either same day or when called back.
Generally, the questions will be simple enough for anyone of reasonable intelligence to answer. The most important part is showing up to the interview appropriately dressed, looking well-groomed, and expressing the right level of emotion. Acting too hyper/distractable or introverted will be a large part of what makes or breaks your interview. Panera looks for people with bubbly but intelligent personalities.