You will have to make a best-guess when you file the extension.
The IRS just wants to know how much you are paying. You can put any amount there, and the extension will work.
The problem for you is that if you underestimate how much tax you will owe (and therefore don't pay enough with the extension), you will be charged interest starting on July 16th.
So you are motivated to file the extension and then get that W-2 or its information as quickly as possible, in order to file the correct return. Note, I am sure you know this, but because the extension is good until October 15th, you can file your return any time before that to cut off the interest.
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