By default, it place place elements of Komplete within C:\Program Files\Native Instruments, and within that, it creates 2 more sub-folders, 1 for 32-bit, and 1 for 64-bit, so the Komplete path for the plugins is:
C:\Program Files\Native Instruments\VSTPlugins 32 bit
C:\Program Files\Native Instruments\VSTPlugins 64 bit
I also kept 32-bit versions of programs and plugins they got rid of, as they keep my memory footprint down when using a live-performance vst-host wrapper called Forte. The 2 I kept are Pro53 and Akoustic Piano. They incorporated them up into Kontakt starting in Komplete 6.
Anyways, if you find the Kontakt5 plugins (there will be 3 of them, for different numbers of outputs), make sure to add that path to the Sonar VST Plugin Manager path list, and either scan, or restart and it should pick up the x64 guys you want.
Bob Bone