To Clock In or Clock Out an employee from the desktop, first open the Users window. Find the employee you want to add the entry to and click Clock In or Clock Out in the Manual column. Note that currently clocked in employees will only show Clock Out, and vice versa.
In the popup, you can now edit the times for the event. If you are Clocking In an employee, only enter a value in the first date and time field. If you want to add both Clock In and Clock Out times, enter values in both date and time fields. You can also include an optional comment, which will appear in any Generated Reports which include this event.
In the calendar/time popup, select the date from the calendar and use the sliders at the bottom to set the time. The bottom-left of the pop has a Now button which will let you set the field to the current time and date.
Once you are satisfied with your time(s) and comments, click the Update Timesheet to save your entry. You will notice that your Timesheets window will now refresh and display your new entry. Note that if you set a Clock Out time to be earlier than the Clock In time, this will result in negative hours worked, so be sure to adjust the entry accordingly.