Yes, if you sold at a gain you will pay taxes on that gain, unless that rental property was your primary residence for at least 2 of the last 5 years you owned it, and the gain is less than $250K if filing single, or less than $500K if filing MFJ. When you report the sale in the SCH E section of the program, it will take care of all that math for you.
Now knowing that the gain will increase your AGI and can potentially put you in a higher tax bracket for the tax year, if you reasonably believe that gain will increase your tax liability by more than $1000 or more than 10% of your tax liability if you hadn't sold it, then you should go ahead and pay an estimate now. If you send the IRS at least 20% of what you estimate your gain to be, then come tax filing time you'll be fine. You can pay the IRS now, online at
http://www.irs.gov/directpay. If your state taxes personal income then you'll need to pay state estimated taxes to your state separately. How you do that, depends on the state, as not all states offer an online payment option.
