Zoho Commerce deals with physical stock of the product, whereas Zoho Books or Zoho Inventory deals with accounting stock.
Physical stock includes Shipments (for stock out) and Receives (for stock in).
Accounting stock includes Invoices sent (for stock out) and Bills raised (for stock in).
If you'd like a personalized walk-through of our data preparation tool, please request a demo and we'll be happy to show you how to get the best out of Zoho DataPrep.