Yes, you should adjust the cost bases of each transaction one by one. There is no way to update them as a batch, and your cost basis per share would be different if the sales were coming from different lots.
You can also report them by grouping them into long-term and short-term transactions and reporting the totals from each section rather than importing them. If you do this, you will need to include a pdf of your 1099-B with your return.
