I have Covered call options that lost money. Fidelity will enter a zero for cost basis on these with the loss amount as the proceeds. How do I correct this ?

There are a couple of options (no pun intended), that you might try that should eliminate this experience. 

These particular steps may provide the ability to post a negative value to form 1099-B, Box 1d.

1. Select the option for a 1099-B
2. Select to type it myself
3. Enter Bank
4. I'll enter one sale at a time
5. Enter the stock data and leave 10d BLANK
6. When you hit Continue you will get a RED error message
7. At the bottom of the screen select Allow me to continue with incomplete information  > Continue
8. Any less common items will be blank.  Select Done
9. No this is not employee stock
10. Select the last item An adjustment is required for reasons not already covered.
11. Enter the negative number that you had in Box 1d.
12. This will complete the transaction

Another option is to put $1 in the proceeds box and then add that $1 to the negative gross proceeds as your cost basis (positive figure). This will provide the accurate results of income and tax.  The most important thing is the correct end results on the tax return.

I have the cost/proceed amounts for the covered call . Can I enter in the cost and proceeds both positive numbers and the gain/lost column would have the correct negative number ?

Yes.  Entering the actual cost and proceeds for your covered call(s) should produce the same results for your return.