Yes you can still use check-in even if you are not using Whova's registration. If you do not use, it will not prevent anyone from using the app. This feature is available to anyone using the app and is meant to replace paper check-in if that is something that you and your team typically do. The check in is very easy.
You can use from your smart phone in the 'admin' icon and you can also use on your organizer dashboard in Attendees > Check-In. Simply find the attendee on the list either by scrolling, typing name in search bar, or scanning their QR code (QR code scan is only available on the app for this). Then you click 'Check-In'. After You've checked in all your attendees for the event, you can export this list of checked-in (or non checked-in attendees) to an excel sheet.