The thing with 1099 is you don't pay tax upfront. You pay your taxes quarterly, you pay what they call estimated taxes. Quick googling gave me some forms. My suggestion, get help from tax professional and may be from next time you can do it yourself. Also, save your invoices, bills, receipts etc., unlike W2 there are a lot of things you may be able to deduct, since you are an independent contractor.

http://www.ehow.com/how_6866383_pay-taxes-1099-form.html