Thanks for the reminder that I've been meaning to rename my Kontakt versions too. In the Browser, clicking on the Plug-ins button opens a drop down with one option being "Manage layouts." This is also an available from the synth rack drop down menu when pressing on the "+" button. Either pathway opens the Plug-in Manager.
Selecting VST Instruments in the first list window allows display of the Kontakt 5 instances in the second window. Mine were also all named "Kontakt 5." Clicking on one instance in the list window selects it. Then look lower down at the "VST Configuration" section and click on the "Plug-in Properties" button.
From the properties window, click on the "Details" button to see specifics. One of my instances has 64 outputs, for example, while another has 16. Trying to rename within the details window does not work. Close the details window. Now in the Plug-in Properties window, type in the number of outputs in the name box. On exiting the box, the Plug-in Manager refreshes the list and now shows the new name. Repeat for the other instances. Now the new names persist in the Plug-in Manager lists. But I found they were not yet displaying in the "add synth" tool. Closing and reopening Sonar fixed that. Perhaps refreshing the VST scan might have done the same. But after restarting Sonar, I now can see different names for each version of Kontakt. I've seen other threads about the difficulty of the different versions of Kontakt showing up with identical names as the default, so we are not alone.
Hope that works for you.