When self-employed the general rule of thumb is to send the IRS 20% of your *GROSS* earnings each quarter. Then come tax filing time you'll be fine. If your state also taxes personal income, then you should send your state an amount equal to the percentage rate your state taxes personal income at. That's anywhere from 5% to 8%.
Then when you file your taxes and complete the SCH C you'll find that after taking into consideration all your deductible business expenses, your "true" tax liability will be within $1,000 either side of the total quarterly payments you already sent to the IRS. So if you're on the bottom side and owe more to the IRS, it will be less than $1,000 and one should be able to just "write the check" and be done with it.
For me, I've been self-employed for 15 plus years now and I follow this 20% rule. Only twice in all my years of self-employment have I ever owed more at tax filing time, and both times it was actually less than $500. I just wrote the check and moved on with life.
