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Can I cover a short sale with the stock I already own?
Yes you can.  This is known as a short selling against the box.  In the old days, this was used to delay a taxable event.  You could lock in a gain without triggering a taxable event.  Any loss on one side of the box would be offset by a loss on the other side, and vice versa.  However, the IRS clamped down on this, and you will realize the gain on your long position as soon as you go short on the other side.  See http://www.investopedia.com/terms/s/sellagainstthebox.asp. As to how to initiate the short cover, just transfer the long position to the same account as your short position and make sure your broker covers the short.  Should be relatively easy.