Quarterly tax payments and tax filings can be two different things. Making the payments "as you go" is what the IRS requires. That means that as you go through the year, you need to pay taxes on your projected profit. At the end of the year, you are required to file your income tax return. When filing the return, you reconcile what you paid through the year with what you owe.
Determining what to pay and when is crucial to avoid penalties and interest on underpayment of tax. Here is a great resource on how to pay estimated taxes.
Hope this helps!
Cindy