I always just renamed each of the Kontakt versions that show up in the list, based on the number of outputs each has, which can be seen in the Properties>Details of each of the 3 dll's.
So, I end up with Kontakt 5 - 08 Outs, Kontakt 5 - 16 Outs, and Kontakt 5 - 64 Outs. For instances where I know I will have only a single instrument loaded, I always select the one with 8 outputs, and when I am building an instance that will contain multiple loaded instruments, I always choose the one with 16 outputs.
There are some trade offs between using multiple instances when dealing with a lot of instruments to place within some instance of Kontakt, and I have found that the 16 output Kontakt version serves me well in the balance of it all, so that is my go to version, and even there I load each Kontakt instance with no more than 6 instruments.
Whatever works for you is fine - the above meets my needs well, so that is how I have evolved to approach it.
Best of luck with it all,
Bob Bone