N11C should be filed for paying late fees.
11C - states that all penalties under section 271(1)(c) will be deposited in this. What is section 271(1)(c) is discussd later.
N11C - states that all penalties other than section 271(1)(c) will be deposited under this code.
This states that except 11C is specific for only one section and N11C is for all other sections.
Section 271(1)(c) - empower to Income Tax Authority to levy penalty under the Act, if the assessee officer or commissioner appeal or the principal commission during the any proceeding is satisfied that assessee has concealed the particulars of his income or furnished inaccurate particulars of income, he may direct to Assessee shall pay by way of penalty ,sum which shall not be less than but which shall not exceed three times amount of tax sought to be evaded by reason of the concealment of particulars of income or furnished inaccurate particulars of Income. In other words, Income tax authority may levy penalty, if any of the following conditions has satisfied.