He was hiding the income to avoid paying the taxes as the company was having some financial difficulties.
I remember him telling Skylar how he felt everyone working there was like a family and he couldn't let the business go under so that was his motivation.
I don't think he was doing anything in particular with the money but his ain reason was avoiding taxes.
The business was making a profit on certain accounts. This income is taxable. By hiding the income Beneke didn't need to pay the taxes. I believe Skylar said he was recording the income as expenditure. Expenditure isn't taxable on Benekes side of the transaction. More information on these types of taxes can be found here : http://en.wikipedia.org/wiki/Corporate_tax_in_the_United_States