When recording payments in Bill.com that you have paid by other means and already recorded the payment in QuickBooks you have the option to 'Do not sync' in the payment confirmation screen in Bill.com.
Please click on the link for more information:
In addition, you can consider posting the payments first in Bill.com, syncing them to QuickBooks and matching them to the transactions that you download from you Bank.
Please refer to the Help menu in QuickBooks for additional instruction for matching online banking transactions to existing transactions in QuickBooks
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