Is there a way to prevent double-counting for auto-payroll? It's coming through payroll and again through bank. Also, how to fix these double entries retroactively?

I can think of a possible solution, askvortsova. 

Since your bank is connected with QuickBooks, the transactions are automatically downloaded to your account. Therefore, there are transactions in your banking transactions that aren't matched yet or that were categorized directly. To prevent double counting for your auto payroll, you'll have to undo and match it to your existing transactions. 

Here's how: 

1. Go to the Transactions menu located on the left navigation panel and click the Bank Transactions. 
2. Under the Categorized tab, undo the transactions. 
3. In your For Review tab, match the transactions to your payroll transactions by clicking the Review. 
4. Press Find Match.
5. Choose a transaction to match your transaction, and then click Confirm. 

Furthermore, you can reconcile your accounts after following the steps above: Reconcile an account in QuickBooks Online.

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