Hi Claire061
Allocating bank transactions to account is effectively creating a spend money/receive money transaction for that amount, it will certainly create double ups if you are also recording the payment manually.
The bank transaction can be matched to open invoices/bills to close them off, this also saves data entry. Bank transactions can also be matched to transactions manually recorded in the software. I would highly recommend going through this Help page - Working with bank transactions, which explains what you can do with bank transactions.