Like Karen, I am careful to mention the extra charge during the M&G. I also try to state potential additional fees in my profile [but of course, not everybody reads through it all too carefully, eh? haha].
There are the scenarios for adding fees that I have used:
DURING BOOKING
If we know about it beforehand, I add it on to the initial booking as a 'Cost Adjustment.' Easy peasy!
DURING STAY
If something comes up during the stay, I first message the owner to let him/her know the situation. The owner may negotiate/reason with me, and then if we agree that an additional fee is warranted, I add it to the booking via the 'Extend this stay' link. It will ask for new dates, but if you aren't actually adding days, you can just make it look like the last day [eg, 9/1 - 9/1]. And then it'll start a new thread with the owner, and you can edit the booking to just have the correct fees before asking the owner to book.