Paying of income tax through challan and filing of return are 2 different things.
1. You can pay challan online or manually.
It is mandatory for the following types of assesses to pay tax online with effect from April 1,2008.
a) All the corporate assesses.
b) All assesses (other than company) to whom provisions of section 44AB of the Income Tax Act, 1961 are applicable.
2. You can file return online or manually (paper forms)
E-filing of I-T returns is now mandatory for assesses having taxable income in excess of Rs 500000/- and All Audit cases.
You have to quote BSR code, Challan serial no, date of challan etc in the return.