Hi ChrisD55,

If you connect a bank account or upload a CSV file, the transactions will show up in the For Review section of Banking. Since you have been manually adding payments and bill payments in QuickBooks, these bank transactions will likely show a Match to a current QuickBooks transaction. You will have to ensure that the transactions are matched up correctly. 

The transactions will only double up if you select Add instead of Match for the transaction on the For Review section, while that specific transaction has a manual QuickBooks transaction. In case you don't see the Match link under the Actions column, simply click on the transaction and select Find Match, which will bring up manually entered QuickBooks transactions that you can match to. 

Connecting the bank account or uploading a CSV file will also make reconciliation much simpler, as matched transactions will automatically be opted in as 'partially reconciled' to the specific period's reconciliation. In the reconciliation screen, you will also be able to see manually added transactions that aren't matched to a bank transaction, and use this information to figure out if this manual transaction is a duplicate, or to figure out if you've missed creating a manual transaction.

Hope this helps!

Bonny