Your cost basis is what you paid for the shares. You've indicated that the current value is less than your basis, so if you sell the entire position at the current value you would have a net capital loss, not a gain. The sale of the uncovered shares is reported separately from the sale of the covered shares and it's possible that you could have a gain on one and a loss on the other. The covered shares could also be split into long-term and short-term shares depending on whether the particular shares were held for more than one-year. (It's also possible that some uncovered shares could be short-term if they were not originally purchased within the particular account.
As Bsch4477 said, the Forms 1099-B that you receive will show each of these lots separately.
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