Hi @skagitsteelheadh, I work for a SaaS company that precisely imports Airbnb reservations into Quickbooks (https://www.bnbtally.com/airbnb/quickbooks/integration). Our customers are primarily accountants who have clients with Airbnbs and wish for more precise accounting. I'll be glad to share how they generally do things.
In short, most accountants account for the 3% host fee directly by subtracting it in the invoice created for the reservation. When a reservation income is received from Airbnb, we create an invoice in Quickbooks. Let's say we have a reservation total $100, within the invoice, we break down the following line items...
We do it this way since Airbnb automatically subtracts the host fee from the payment. Each line item goes into it's own Product/Service code that we set up in Quickbooks. For more information about the Chart of Accounts generally used for an Airbnb rental arbitrage business model, I've written an article with templates you can download, which you my find helpful: https://support.bnbtally.com/en/articles/3571867-preparing-quickbooks-for-an-airbnb-rental-arbitrage...
For reconciliation, once the money from Airbnb is received into the bank account, the invoice is reconciled with the deposit. Sometimes more than one invoice is reconciled with a single Airbnb payout since Airbnb tends to lump more than one reservation into a single payout. In most cases, our accountants use a payment clearing account to pay the invoice and then transfer the money from the bank account.
Overall, of course there may be more specifics as it pertains to your specific business but I hope this serves as a start to answering your question.