That's not quite how it works. You file one return, and your net 1099 income (minus expenses, if any, which I assume are going on Schedule C) is added into your total taxable income -- added with your W-2 income. You don't file a return for W-2 income, get a refund and then file again to pay the tax on the 1099 income.
The first thing I'd be concerned about is that if you haven't paid estimated quarterly taxes on your 1099 income, you need to make sure you've had enough withheld from your W-2 income to reach "safe harbor" provisions for avoiding penalties for underwithholding.
For most taxpayers (except those at rather high income levels), there are three ways to be in "safe harbor":
* If the amount of tax withheld is at least 90% of the tax due this year;
* If the amount of tax withheld is at least 100% of last year's total tax liability;
* If the amount you still owe the IRS is less than $1,000.
If any one of these applies, there will be no penalty for the underwithholding.
If your W-2 income would have been overwithheld absent the 1099 income, then some of what *would* have been a tax refund would instead go to paying the tax due on the 1099 income not yet taxed. A lot of households that have a mix of W-2 and 1099 do this -- overwithhold intentionally on the W-2 income in order to cover the taxes that would be due on the 1099 income, and thus avoid the need to file quarterly estimated payments.
"Hey, for every ten dollars, that's another hour that I have to be in the work place. That's an hour of my life. And my life is a very finite thing. I have only 'x' number of hours left before I'm dead. So how do I want to use these hours of my life? Do I want to use them just spending it on more crap and more stuff, or do I want to start getting a handle on it and using my life more intelligently?" -- Joe Dominguez (1938 - 1997)