The answer varies depending on your policy and in the [Channel Managers >] menu on your you can follow the steps bellow:

Compatible Configuration
I linked my Stays fees with BookingIf you have linked the fees on the [Settings > Fees & Taxes], in this case, we will follow the same configuration you used when creating the fee on Stays.
I did not link the feesIn this case, you will need to choose the invoice you want in this configuration below in your panel, on the [Finance > Relation with Fees & Taxes] menu.

Now that you already know how to choose the invoice in which Booking fees and taxes will appear on Stays reservations, how about checking out more related subjects?