In the article below, you'll find information on the two ways you can activate automatic check-in for your users.
Auto-clock when you create a new shift
It is possible to Auto-clock a specific shift by clicking the auto-clock checkbox when you create a new shift.
A good use for this option would be for an employee training when you don't want him to clock in/out.
Automatic time and attendance via employee profile
It is also possible to activate automatic clocking to an employee's profile for all their shifts via HR > Employees and the Settings subsection in an employee's profile.
If your employee's clockings doesn't seem to be transferring their timesheet correctly, here's an article that might shed some light on the subject.