Recording receipt against Export Invoice is same as recording receipt against normal invoice. Lets see how to record such receipts:

Go to Income > Receipts

Please click on New Receipts

Select tab Against Invoice . Fill up the fields as follows:

Money Received from : Select the customer from the drop down from whom has the payment is received.
Receive date : Enter the date on which the payment is received.
Deposit to Account : Select the account from the drop down.
Receipt Mode : Enter the receipt mode - Cash/ Cheque/ Credit or Debit card / Internet Banking
Description : Can mention any information relevant.

Click on save and its done .

Your receipt against the Invoice is saved. You can edit and print the same.

Another way to save the receipts on export Invoice is , click on the invoice against which you had received the receipt . your page will look like this:

Now click on "Add payment"

Fill all the details with the details of exchange rate as show in above screenshot.

Click on save and its done .