Once you have uploaded your csv file, next to the transfer, click the Options button.
From the drop down menu, choose the 'Explain' option.
Click on the 'Match' tab.
If there is an invoice in the portal that matches the value of the bank transaction, they will be listed for you to click the Match box to choose the relevant item.
Once ticked, providing the target total and the total amount agree, click the 'Explain Transaction' blue button and this will allocate the receipt against the invoice and mark the invoice as paid.