Undeposited Funds and Transfers counted twice on my bank register

Hello there, BrianConstruction.

I'll share some details on how you can fix your balances. If you already added the downloaded transactions, you'll want to undo them by following these steps:

1. Go to Banking or Transactions on the left panel. 
2. In the Banking tab, click the Categorized or In QuickBooks tab.
3. Find and put a check mark on the transaction that is making your balance off.
4. Select the Undo button. This will add the transactions back on the For Review tab.

Once done, find the transaction you have recorded in QuickBooks and make sure that it is deposited it to the Undeposited Funds account. Create a bank deposit in QuickBooks to add the transaction to your bank register.

For example, a customer bought an item worth $300, and you entered it as a sales receipt. Then from the Deposit To drop-down menu, you've selected the Undeposited Funds account.  

After you receive the payment, you can create a bank deposit. Please make sure to select the bank account where the transactions are downloaded.

When you have the payments downloaded from the Banking page, you can just match it to the deposit you've recorded in QuickBooks, so you have an accurate bank balance. 

Finally, you can start reconciling your account.

I'm adding this article for additional details: How to Use the Undeposited Funds Account to Receive Payments in QuickBooks Online.

Please let me know if the steps help fix your bank balance. I'll be around to help you out again.