I'm not a tax professional, but I do do a lot of taxes of various forms by myself. So in emcee, this is based on being self taught, and might not be 100% accurate. Given that, I believe you do, but do include cost that you spent as a part of capital expenses. As for when - that depends on what the percentage is. Typically you want to pay 90% of the taxes owed up to the point by the end of each quarter to avoid fees, however this is the final quarter, so as long as you can mention the sale being in the final quarter, you can pay it as a part of your final tax submission.