I am entering the sale of a second home I sold last year. Under the "proceeds" do I enter in the net amount I received from the sale after all the closing costs?

[martinmsm]

Or do I enter in the gross sale amount?

[Opus 17]

It should not say "proceeds", it should say "Selling price."  You can add certain closing costs to your adjusted cost basis, but not all closing costs.  There is a list in publication 523. 

https://www.irs.gov/pub/irs-pdf/p523.pdf

Your profit is also not affected by any mortgage.  If your selling price was $100,000 but you only received $50,000 because there was an outstanding mortgage, your selling price for the capital gains calculation is still $100,000.