There are several options when you're ready to check in attendees to your event. You can check in many people at once by using the Actual Attendance/No Shows option.

On the event's Attendees tab, click the down arrow next to the Add Registration button and select Actual Attendance/No Shows.
 

This will open the Edit Attendance/No Shows window.

You can click the Set all to Attended button to mark all as attended, then individually change non-attendees to No Show or Unknown. Alternately, you can go through the list, and select the appropriate status for each individually.

Click Done when the attendance updates are completed.