income tax returns filing

File ITR 3 with books of accounts, commission earned as gross income.

1. It is a common practice for commission agents to receive the sale proceeds or fees on behalf of the principal and remit the same after deducting the commission amount. 
2. This practices even though accepted but still raises a doubt among the Department due to a huge amount of cash deposited and withdrawn. So, for the purpose of maintaining accountability and clarity in accounts, it is better to maintain proper books of accounts specifying the invoice date and remittance to the principal on a regular basis to avoid any kinds of confusion in the future. 
3. ITR -3 can be filed in your case. 
Please correct me if the above solution has an alternative view.