TradeGecko’s QuickBooks integration allows you to split your sales invoices across multiple sales ledgers. You can choose to send sales invoices to a ledger based on the SKUs on the invoice (this splits the invoice by line item). Refer to this article on How to Assign Default Sales Account by Variant.
The table below shows how elements of a Sales Invoice sync over to a QuickBooks Bill.
For credit notes, understand the sync details between TradeGecko and Quickbooks by reading this article.