Do I add short-term or long-term transactions when adding 1099-B form?

Your 1099-B should have subtotaled all of your sales by Sales Category.

You will need to enter each sales category separately. Short Term Covered would be one subtotal; Long Term Covered would be a second entry; Long Term Noncovered (if you have it) would be a third.

The IRS needs the information about which sales are short term and which are long term, since the taxation is very different for those two categories.