No,You can load 16 instruments in one instance of Kontakt.
Load kontakt,then drag and drop the instruments into Kontakts main window,(see manual and videos,..hint,hint)
A seperate midi channel is usually assigned incrementaly as you add each instrument.
In Ve Pro set the midi port to 'Vienna Ensemble Pro midi port 1' and set midi channel to 'omni'.(see manual)
each time you add a new instance of Kontakt you assign different Ve Pro midi port to that instance,for example a 2nd instance of Kontakt would be assigned to 'midi port 2' another instance 'midi port 3 and so on ,In Protools you can assign 64 ports (32 ports in 32bit server and another 32ports in 64bit server add 64 instances in just one instance of V Pro! thats 512 instruments in one instance of Ve Pro,again thats in Protools!