Can I perform check-ins at the Organization level?

Organization Managers can perform check-ins from either the Schedule or the Opportunities tabs in a user's profile. The tab the action is in depends on the type of check-in enabled for the Opportunity. 

org opp tab

If an Opportunity has General Check-in enabled, then the Organization Manager can perform the check-in from the Opportunities tab. Since General check-in does not match the in and out time against a shift, the check-in buttons are found in the Opportunities tab. 

org sched tab

If an Opportunity uses Shift check-in, the Manager will perform the check-in on the Schedule tab. Performing the check-in at the Organization level will still map the in and out time against the shift. It will still follow the Opportunities-specific attendance settings, such as auto-assigning hours.