How do I deactivate the pop-up flash on the Nikon D7000 when using a flash unit that is mounted in the hot-shoe?
Check to see if custom setting e3 is set to commander mode. If so the camera thinks you want to use the pop up flash to control slave units. You need to change the mode to any of the other options: TTL, Manual, or Repeating. This is covered on page 223 of your owner's manual.
If that is not it, make sure the external flash in powered on, and that it is compatible with your camera. If the D7000 does not detect it and the camera is in a mode that activates flash automatically it will pop up the built in flash. Even if the camera doesn't detect the external flash it should still trigger it but you will have to choose a mode that doesn't automatically activate the built in flash. Try one of the PSAM modes. Since you're going to need to set the flash power manually in this case, you might find Manual mode will allow you the most control. You might also want to turn off Auto ISO sensitivity since the camera won't know the flash is going to fire.
If you are using a third party flash, be sure the trigger voltage of the flash is not higher than your camera can accept or you could permanently damage the electronics of your camera. See the answers and links to this question.
If the built-in flash has popped up, push it back down. With a hotshoe flash attached, it generally should stay down.
If it pops back up, then try P, A, S, or M modes. It should not pop up automatically in these modes.
Still pops back up? You have the option of using the No Flash exposure mode
Failing that, as Michael Clark suggested, check the commander mode settings and turn the flash off there.