I can provide some answers to your questions below....
Is there a way to change amount of 2nd homeaway payment? Need to remove cleaning fee.
Yes, you can modify the reservation after it has been received. In this case, you'll want to build a new quote for the reservation in question, keeping everything the same but removing the cleaning fee. You can set this quote as the "terms" of the reservation and your payment schedule will automatically be updated. The scheduled second payment will be reduced by the amount of the cleaning fee.
The easiest way to accomplish the above is by opening the reservation in question and selecting "Modify Terms" from the large action menu in the upper right. You'll be asked if you want to build a brand new quote or start by copying an existing one. I would recommend copying the existing quote on the reservation as a starting point. Make the necessary adjustments to the quote and save the quote, thereby setting it as the terms of the reservation. The reservation payment schedule will be updated at that point.
Also, what is the stripe application fee? Was charged on last reservation.
The Stripe application fee is where we add the MyVR processing fee for the reservation. Since this reservation came through our Channel Management offering, we charge a 1.49% channel management fee for the reservation. If there are any refunds or deposits returned on the reservation, the processing fee is refunded for this portion for Stripe accounts created before Sept. 14th 2017. You can read more about our HomeAway channel management offering here:
Let me know if I can provide further clarification.