If you have income tax withheld from the conversion, you will avoid any penalty related to the conversion. Withholding is treated as if it was spread out over the whole year.
If you don't have taxes withheld, you need to follow two steps.
1. Make an estimated payment at www.irs.gov/payments before January 15.
2. When preparing your tax return, enter the penalty interview (even if not automatically prompted) and prepare the penalty form 2210 using the "annualized income" method. You will need to list your income and tax payments by quarter, and show the IRS that even though your tax payments were not evenly distributed over the year, they were appropriate for the amount of income you received in each quarter. (Or in your case, you may end up showing that you were $250 short each quarter, but not thousands short.)
You can also have the taxes withheld by making the conversion in two steps.
1. Make a direct rollover conversion with taxes withheld.
2. Within 60 days, send a payment to the Roth IRA custodian in the amount of the missing taxes, telling them this is also a conversion.
For example, to convert $10,000, you could directly convert $10,000 with $2000 withholding. Then, within 60 days, send a check for $2000 to the Roth IRA telling them this is also a conversion. (They don't need to know or care that it is part of the same conversion.) In other words, since you must have the $2000 on hand anyway to pay the tax, have the tax withheld and deposit the tax money as part of the conversion instead. This removes the need for the annualized income method to avoid a penalty.
If you don't have money on hand to pay the tax, then do the conversion with withholding but don't top it off. If you convert $10,000 and you think you are in the 12% bracket, have $1200 withheld. You will tell turbotax that you converted $8800 and "did something else" with the $1200. The withholding will be to your credit on your tax return.
If you had extra withholding, to cover the SE tax, that would eliminate that penalty as well. For example, if you are single, with self-employment of $14K, and the standard deduction is $19K, you could convert up to about $48K and stay in the 12% bracket. (or convert just $5K and pay nothing). If you converted $48K, you would have $5760 withheld. If you added the SE tax and asked for $5900 of withholding, that would cover everything.
