After the setup launches it would ask you for the language selection. After that you would be presented with a window which would allows you to install Windows or launch the 'Repair computer' wizard. Now just press Shift+F10, navigate to the other partition and launch setup.exe manually.

If you need, use diskpart to list available volumes:

  diskpart
  list volume

If the second, NTFS volume somehow don't receive a letter (and hence you can't navigate to it):

  diskpart
  list vol (note the number of the volume)
  sel vol ## (the number of the value)
  assign letter=K (or any other to your liking)