The advanced settings section allows you to configure what payment section (rent commission, owner rent or both) will be used to apply the adjustment, discount or coupon. Also you can choose when the adjustment, discount or coupon should be applied (down payment, remaining payment or both). Please note that for amounts calculated by a percentage (i.e. a coupon) the base amount for the calculation will still be the full amount and not the rent commission amount. This setting only tells Kigo what section of the payment details should be used.
Suppose you want to have a coupon to discount 10% only of your rent commission, which is 20%. If the total rent for the booking is 200, your rent commission will be 40 (20% of 200) and the coupon should be 4 (10% of 40). In this situation what you need to do is to calculate the percentage of the coupon with the total amount, in this case 4 is 2% of 200. Thus the following setup should be done: set the coupon to 2% and "Apply channel partner rent adjustments, discounts and coupons to" to rent commission.