Now before anyone says "of course", keep in mind I will not be gaming on both monitors simultaneously. 1 monitor for gaming the other for Internet browsing etc.
Will this significantly lower my FPS if my graphics card is running a second monitor desktop?
GPU = GTX 780 overclocked Single card - not SLI
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No not at all. However with most games the second screen will just be black when you are gaming. So you will not be able to use it during a Full Screen game.
It should be minimal. Someone from HardForum.com test his rig with one and two 1920x1200 monitors attached. With the 2nd monitor attached I believe he stated the drop in performance was like 3%. This was around 2 or 3 years ago.