First of all, fire your CPA. Sounds like that will help you pay off the debt faster. If you can't find a better/cheaper CPA in NYC, Turbotax online has a special version for contractors, which is what I use.

Next year, make estimated quarterly payments to the IRS, Just take 30-40% of what you make each quarter and send it to them, their website explains how to do it. Then at the end of the year you will either get a refund, or the amount you owe will be small enough that you can easily pay.

EDIT: I use Turbotax online, not Quickbooks online.