I'd be happy to help you in correcting your EFT payments, so you'll be able to reconcile in QuickBooks Online.
Are these transactions downloaded from your online banking and added it to your QuickBooks Online account? If so, you can Undo the downloaded transactions and Match them to your manually recorded customer payments instead of adding them to your QuickBooks. This way, it will not duplicate the transactions while reconciling.
To match transactions:
On the Banking page, select the For Review tab.
Locate a transaction with one or more possible matches to review.
If one match was found, the matching transaction appears in the Category or Match column.
For a transaction matched to a single record, if the match is correct, from the Action column, select Match to accept it.
For a transaction matched to multiple records, from the Action column, select View to open the transaction row, review the possible matches listed under Records found, select the correct one, and select Match to accept it.
If the possible match is not correct, select the transaction to open it, and select Find other records to open the Match Transactions window and search for other possible matches.