In order to allocate a transaction to an invoice in the bankfeed window, use the the tab Match or Create 
More info: Working with incoming bank transactions in Accounting

Option 1 -  Match

1. Choose Match to allocate the transaction to the matching invoice(s).
   • a list of all your invoices, payments, receipts and credit notes will be displayed. You are being asked to choose the transactions that make up a particular amount
   • Transactions can be filtered in a chronological or alphanummerical order according to Date, Number, Contact, Type, Reference, Due Date, Amount and Outstanding by clicking on the appropriate header
   •  Search for the matching transaction by clicking in the search field. Search for: 
     • Sales invoices
     • Customer receipts
     • Credit notes
     • Expense refunds
     • Other receipts
     • Bank transfer
   • NOTE: Only unpaid and partially paid invoices, payments and receipts will be displayed. Match found will be displayed in cases where the date and the amount of the transactions matches the unpaid invoices, however, only if there aren't multiple invoices matching the same date and amount. 
     Note as well that you can match receipts/payments partially to invoices, but you cannot match receipts/payments partially to Other receipt/Other payment transaction type. In this case, you can only match the full amount of your receipt/payment to the Other receipt/Other payment transaction recorded.  
      
2. Tick the appropriate box to match the transaction
3. Make sure that the Left to match (make adjustment) is 0. It will show how much is still outstanding. This can be adjusted by clicking on (make adjustment). Also, use (make adjustment) if the customer, for example did pay the invoice in full but the bank charged a fee resulting in a lesser transaction showing in the bank statement, record the expense incurred via the option Make adjustment. This will record the fee as Other Payment and record the full receipt against the invoice
4. Click Match            

NOTE:

• An unpaid invoice will register the payment in the banking activity. It will also mark the transaction as cleared (which means that it has been imported from the bank) which will facilitate the reconciliation process
• A paid invoice can in theory be deleted from the bankfeed by clicking on the X in the upper left hand corner of the transaction, however, it won't show as cleared in the bank activity

If neither created an invoice nor a payment or a receipt, create the payment and/or receipt within the bankfeed, by clicking on

1. New Transaction
2. Select Payment on Account 
3. Select Add

 Later match this transaction to an invoice.                                                                                                                

 
Option 2 - Create

If the invoice that need to be allocated to a transaction has not been created yet, a payment can be created on the account.

1. In the field For, select the contact, customer or vendor.
2. In the field What,  choose between Payment on account or Other Payment
3. Select Tax Rate if applicable
4. Create

You can use this option for further situations:

• the amount received or paid doesn't match the invoice: a partial payment for example
• the invoice still needs to be allocated to a credit note

The allocation can be done once the payment on account has been recorded in the customer's or supplier's account. 

Option 3 - Transfer                     

This option allows you to record a bank transfer from one account to another. 

NOTE: Please note that cash deposit cannot be recorded using this option. You will need to discard this transaction from the list and record it manually from the cash account: Record bank deposits in Accounting  

CAUTION: Other Payment/Receipt is a standalone transaction: This means once created and imported into Accounting you won't be able to match it to an invoice (it includes the ledger and vat information and duplicates with the information already recorded in the invoice) 

1. In order to correct an accidentally falsely created other payment or other receipt, delete it from your bank activity window
   • Make sure you keep note of its description, amount and date 
   • Please check How to delete a bank transaction in Accounting
2. Create a payment or receipt from Banking and allocate it to the invoice
   • From the banking tab, create a new entry, but this time make sure that you create the correct type of entry:  Expense payment or Customer receipts
   • ​​Alternatively you can register the payment from the invoice

NOTE: Note: these transactions won't be shown as cleared in your bank activity. See About bank reconciliation