A cheque received by the CRA can be mistakenly applied to current year instalments rather than to tax payable. How can this be avoided? CRA responded:
[W]e suggest that taxpayers send a remittance voucher with their payment rather than a letter. Those remittance vouchers are personalized, coded with taxpayer information and attached to the statement of account sent, thus ensuring that payments are applied to the correct account and taxation year.
Customized remittance vouchers for businesses can be obtained quickly and easily through the CRA Web site … or through the "My Business Account" service … .