You don't add up all the gains and losses and put the net result on your tax return. You have to report the individual sales on your tax return. TurboTax (or whatever tax software you use) will add them all up and calculate the net loss. Up to $3,000 of the loss will be used to offset other income, reducing your taxable income. The remaining loss will be carried over and used to offset income in future years. It's called a capital loss carryover.
So if you don't have any significant capital gains for the rest of this year, the net loss will reduce your tax. You will not pay any tax on the gains that you had earlier in the year, and you will not have an "April nightmare surprise."
