It's imperative to deduct the right amount of money for your business (and to avoid any unpleasant surprises from Uncle Sam). Check out the IRS Web site and use one of their online withholding calculators to determine how much money you should set aside for your taxes, or consult with a good accountant.
Be sure to get the right tax forms too: Schedule C (Profit or Loss from Business) and Form 8829 (Expenses for Business Use of Your Home) are the main forms for home-based business owners.