When payment is made, Accounts should inform you of the receipt of an unmatched deposit. If this relates to penalties only, send a completed form CAS 16 to Accounts (remember to include your allocation code in Part 2 of the form, so that it is returned to you). Accounts will return the form, confirming in Part 2 that the charge has been raised and the payment matched. The CAS 16 can then be filed with your papers.
If the payment also relates to tax and interest, the tax and interest should be brought to account in the normal way, by using COMPASS ( IHTM31111). But you must make sure that the interest exactly matches that included in the letter of offer ( IHTM36338). The appropriate amount of the deposit should be applied to tax and interest. The balance, which should equal the penalties negotiated, should be brought to account as above.