YNAB allows you to add a specific column for check numbers in account register.
Step 1: Select the account you want to add the check number column to in the sidebar.
Step 2: On the right hand side of the register, you will see a small plus sign.
Step 3: Click on it to see a drop down menu.
Tip: You can also access the drop down menu by right-clicking on any of the column headers.
Place a check next to the word "Check".
A check number column will now appear in the account register.
Did you know that your YNAB register can replace your paper register? If you're tracking your expenses in YNAB, entering them in a paper register is double entry! Save yourself the trouble and let go of that paper register.