This article explains the two ways you can activate automatic clocking for your employees.
Auto-clock when you create a new shift
You can set up auto-clock for a specific shift by ticking the Auto-clock checkbox when you create a new shift.
A good use for this option would be for employee training when you don't want them to clock in or out.
Automatic time and attendance in the employee profile
You can also activate automatic clocking for all an employee's shifts in HR > Employees and the Settings subsection of an employee's profile.
If your employee's clocking doesn't seem to be transferring to their timesheet correctly, here's a troubleshooting article.