Where do I add info about additional rate if not picked up by a certain time on last day of stay?

Boarding is billed on a per night basis, but that doesn't mean the dog only stays overnight. Rover's FAQ states that the "nightly" rate is good for up to 24 hours. So, if a dog is dropped off at 7 pm on one day for a "overnight" then it should be picked up by 7 pm on the following.

The best way to handle billing is to find out the client's drop off and pickup times before the stay has been confirmed and paid. I never have any problem adjusting things initially at our M&G or through messaging with repeat customers. They understand and never quibble. I will allow them a couple of hours leeway but I never tell them explicitly that they can have, for example, two hours free. It invites misuse.

As an independent contractor, you can charge however you'd like. The best thing to do is clarify any variations in your profile. If you only allow drop offs and pickups within certain time frames, then that should be explained in your profile and it is always a good idea to go over everything before finalizing a job.