You can ensure that an after-hours fee is charged for bookings across an entire day for a location in the following manner.

You will first of all need to set the location hours so that the day in question has the office hours set to 00:00-00:00. The AM and PM After Hours will also need to be setup, please see the image below.

You will then need to ensure that the After Hours Booking option has been set to yes and that an after-hours fee has been set for the relevant location. Please see the image below.