On the 1099 B form I have Long term Covered and Covered total. Which do use? I

Both, but separate. Long and short term capital gains are taxed at different rates. 

You will enter the Long term covered transactions, providing the cost basis, date of purchase, sale price and date of sale.

Subtract the long term covered from your total.

You will enter the other amount as Short term covered transactions, again providing the cost basis, date of purchase, sale price and date of sale.