If the payment you sent in was for your income tax owing for tax instalments, you can enter this amount as a quarterly tax instalment. Click on the heading titled Deductions and scroll down to the heading that says "Tax Instalment Payments" You will then be prompted to enter the amount.
If you sent in a payment anticipating the amount that you would owe for your 2017 income tax return, the Canada Revenue Agency will automatically apply this for you once your income tax return has been processed.