Each Shopify Payments payout is sales minus fees and refunds, so it rarely matches a single sale. Upload Shopify's transaction export and see each payout split into the lines to use when you explain the bank deposit in FreeAgent. It runs in your browser: nothing is uploaded anywhere.
In Shopify: Settings → Payments → View payouts → View transactions → Export, choose the dates, then Export balance transactions. Choose that CSV here, or try sample data.
In FreeAgent, open the bank deposit for each payout and explain it with these lines: sales as Sales income, fees as your bank or merchant charges category, and refunds and other lines as your accountant advises. Lines marked "adjustments and other" (disputes, chargebacks, reserves) need a closer look.
Not affiliated with Shopify or FreeAgent. A helper for your bookkeeping, not accounting advice.