Hello there, @thedaisycollective.

You can create a Bank deposit if the transactions were mapped to the Undeposited Funds account. Or a Transfer transaction if Square has its own checking account. This is done to avoid duplicate transactions in the Sales entry.

Here's how to create a Bank deposit transaction:

1. Click the + New button and select Bank deposit.
2. Check the box beside the transactions that are included.
3. Verify the details and select Save and close.

Also, you can check out this article to know more on how to manage the transactions being synced from Square account: Sync Square with QuickBooks Online.

I've added this article for your future task when you're ready to assess your business financials: How to Reconcile an Account in QuickBooks Online.

Please don't hesitate to let me know in the comment section if you need further assistance or other questions. Take care.