At WholeCell, we do not recommend importing every e-commerce order from WholeCell into an accounting platform -- doing that is overwhelming for bookkeeping/accounting and costly. Each marketplace handles payouts differently: some group payouts into weekly, bi-weekly, or monthly deposits, while others send a payout for every individual order.
One option is to have your bookkeeper reconcile these marketplace payouts in bulk. For example, take all the orders from WholeCell for a period from a single marketplace and create one invoice in QuickBooks (or whatever accounting software is used), utilizing a single line item to represent the total of all orders. This invoice can be reconciled against all payments from that marketplace in the period. All individual orders will be stored and retrievable from WholeCell, while the accounting picture is simpler--reducing the cost of bookkeeping/accounting.