How to charge late fee by hour in Rental?

I own a vacation rental home. Everytime customer check-in, I'll will hold the security deposit and return it to them on the checkout day, in full.
Now, my customer ask to extend their stay for another 2 hours after standard checkout time. I charged them USD3 per hour from their security deposit for that extra time.
How to record the extra charge and the return of remaining security deposit?