Are you matching the transactions in the Bank Feed tab? If not, this could be the reason why you see double transactions. No worries, I'm here to guide you through the process of matching the payment to the bill:
Download your bank and credit card transactions.
Review your downloaded bank transactions (Banking > For Review)
3. Click on the transaction to expand the view.
4. Review the Records found. These transactions are ones you already entered in QuickBooks.
5. Select the link next to each record to get more details.
6. Review the Deposit to field on the forms. Your transaction in QuickBooks is already in the account listed.