You can make estimated tax payments for anything, and you won't designate their purpose when you make them. That's because your 1040 just totals up all the taxes you have to pay, then subtracts out payments you've already made, whether through estimated taxes, withholding, or credits.
If you sell a property in another state, you will actually end up paying taxes to both states. Specifically, you'll file a non-resident return in the state whether the property was sold, and a resident return in the state where you live. Your resident state will give you a credit for the taxes paid to the other state, so you won't be double taxed.
Nick K, EA
