Firstly, the default shift settings can be configured in the Admin Console under Settings => Shifts, as shown in the following screenshot. The relevant setting field is called "Work shift". The default settings is for shifts to reset at 12:00 AM. This means that by default if an employee does not clock out before midnight, then their shift will reset. When they would go to the time clock to clock out after midnight, it would only give them the option to clock in to a new shift.
There are two ways to support employees who work past midnight, depending on your scenario:
1) If there is a time of day that you are certain employees never work at, then you can set the workday to start at that time. For example, a restaurant may always be closed at 4:00 AM, so they could set the workday to start at that time.
2) If there are always some employees working around the clock, then you'll want to switch from a workday start mode to a maximum shift mode. Then set the maximum # of hours an employee may work in a single shift. You should not overestimate this value, because if the value is too high, then an employee who forgot to clock out one day may show up the next day and find that they are still clocked in! It would be best to set this value slightly higher than the longest amount of time you would normally expect any employee to work.