You are correct. Your gain is the difference between the selling price and the purchase price, regardless of loans. If you net less money than the purchase price due to a loan, that just means you got some of the money out early.
(Let's take the simplest case. You buy a house for $100,000, all mortgage, nothing down, on Monday. On Tuesday you refinance for $110,000 and pocket the $10,000 extra cash. On Wednesday you sell for $120,000. Your gain (profit) is still $20,000, even though your proceeds are just $10,000, because you got the other $10,000 out early via refinance. )
Your gain is the difference between the purchase price and the sales price. The sales price is recorded in your county records office if you have no idea. If you lived in the home as your main home, the first $250,000 of your gain is tax free and the rest is taxed as long term capital gains. Even if the tax is more than the proceeds, because that just means you took the gain out early in the form of cash out refinances.
If you are in the section for "sale of your home" the program should ask for the sales price, and it also has a smart guide module to help you calculate the cost basis by adding improvements and other items to the purchase price.
