Right now, there is no way to select more than one registrant and check-in all at one. So, please create a check-in button, on the registrants page, just like Publish/Delete/etc buttons, such that, we could select more than one registrant, and check them once.
So you are checking registrants manually, not using a mobile APP? If so, it makes sense. Will work on it and add support for this feature in Events Booking version 3.0.0. Will need about 2 to 3 months for the development of this new major release, though