Don't handle it yourself. Go through a CPA.
Agree with Chimps.
I had a tricky year with business consulting, work in different countries, etc...I had two different ACCT firms do my taxes - one for each country.
I owed a little over $30K. Paid it, and of course, was audited because it was higher than normal. The gov't sees a big change (up or down) and they figure you're hiding something. Triggers the system to flag you.
So I got audited, and the partner at my ACCT firm sent the gov't a letterhead document saying he vouched and signed the tax return files. Not only did the gov't go away, but I got an extra $3K back due to filing conservatively (which my accountant and I agreed upon beforehand, so we had ammo to fire back at the gov't in case they came hunting, which we knew they would do. I wouldn't normally file conservatively...why give the gov't your money to sit on).
By the way, don't hire Joe Accountant who works out of his basement firm. Hire a decent reputable firm. Reptuation goes a long way. Some junior auditor fuckpiece isn't going to want to tangle with a sizeable firm...the paper gets long and it gets dragged out and kills the auditor's closing metrics. It helps to have a big dog in a big fight.
Depends here on how much you tried the fuck the government for. A grand or two? Pay up you cheap bastard. But if this is a 5 or 6 figure tax bill, get a decent accounting firm on it and get your shit together. Then hold on for your life and prepare to put future expenses on hold until you know you've been cleared.