If you want to penalize people for registering past a specific date, you'll need to set up the event with an early bird discount or add-on. In addition, you could set up a non-refundable deposit using partial payments.
You don't need to charge a late fee when you use early bird discounts. The standard price becomes the highest price that someone will pay, which rewards early registrants rather than punishing late registrants.
So, when someone registers before the first date, they'll see the "late" price marked out with the date of the next price bump.
If you need to manually charge a late fee, make sure it's clearly communicated on the signup's page, then create a late fee as an Add-On. Keep the add-on hidden on Church Center so only an Admin or Manager can apply it.
Once a person registers, add the late fee like an add-on, and then send a balance due reminder email.
Expand the attendee's detailed charges to see the late fee listed.