If you both agree to an extra charge, I would just update the reservation to increase the cost. So in your messaging with guest you can say "the cost of parking is $10 per night and I will submit an alteration to your confirmed booking to increase the total by this amount" or something - there is no place for special notations in the Alteration process.
There was, for a brief moment of time, a little tab over the message thread with guests. The tab was "paid amenities" and you could go in and add a request for payment for various reasons. But that must have been a test as it was only rolled out to certain hosts, and it's no longer available.