Thanks for posting here, @userleona.
To further assist you with this, I recommend reaching out to the Shopify support team to check how the sales data from the app sync with QBO. Also, the program (QBO) only depends on the information entered and receives from the third-party app.
For your reference, please see this site: Shopify for QuickBooks Online.
Then, to make sure that your transactions are under the correct account, you can easily categorize them in QuickBooks. For the detailed steps, please visit this article: Categorize and match online bank transactions in QuickBooks Online.
Don't hesitate to post again here if you have concerns with Shopify and QBO integration. I'll be around to help. Keep safe.
