1.) Independence Standalone can use up to 32 MIDI ports with 16 MIDI channels on each port. This feature is needed for situations like " several master keyboards playing several sounds" for example, large arrangements controlled from external DAWs or whatever out of the ordinary situation you may think of. Those situations do not include a host DAW for Independence.
2.) The VSTi plugin version of Independence does NOT NEED more than one port with 16 channels , nor does Kontakt or any other plugin for that matter. The reason for that is that the DAW (host) is capable of providing those different ports, if need be even MORE than the 32 port which Independence standalone can provide.
3.) If you do need more than 16 MIDI channels you need to load a second instance of Independence, which will give you another 16 MIDI channels. BUT the second instance of Independence will NOT give you MIDI channels 17-32. It will give you another set of MIDI channels 1-16. Those can be assigned from another MIDI port which the DAW will provide. Another port usually means another master keyboard (even though there are master keyboards on the market that actually can give you more ports, like Nektar for example), but this is just by the way.
Now lets have a look at the first instance of Independence.
You load your first sound, which will be Layer 1. By default this Layer would be assigned to MIDI channel 1, but this can be changed if needed.
Now you add an second Layer 2. By default this Layer would be assigned to MIDI channel 2, but this also can be changed if needed.
Keep adding Layers as needed, in your case up to 16. Make sure each Layer has it´s own MIDI channel.
Once you have 16 Layers on different MIDI channels your instance of Independence would be - let´s say - "full", at least for your needs at the moment.
Now you load another instance of Independence.
You load your first sound, which will be Layer 1. By default this Layer would be assigned to.....(all the same as in the first instance)
Lets say you want to play the first Layer of the second instance of Independence, which is MIDI channel 1:
If you have the same MIDI port (master keyboard) assigned to both instances of Independence and play on MIDI channel 1, then you will probably hear the first Layer of the first insance of Independence as well as the first Layer of the second instance of Independence. To avoid that you simply have to TURN OFF the Monitor Button on the corresponding Samplitude track of the first instance, as this is NOT to listen to the already recorded stuff, but to the momentarily played stuff. To be save and not get confused you can also turn off ALL Monitor buttons of the first instance of Independence in Samplitude.
I think basically you´re on the right track and all is actually working the way you want. It´s just getting your head around the difference between the direct approach of MIDI port and channel assignement in the standalone version and the assignement via Sammplitude for the VSTi version.
PS!!!: There is NO NEED TO INSTALL a second instance of Independence. Once a plugin is installed you can load as many instances as your computer can handle. The only thing that´s important to know is that you have to load it on ANOTHER TRACK. You CANNOT LOAD multiple VST-instruments on the same track.
So your Samplitude tracks 1-16 would be instance 1, Samplitude tracks 17-32 would be instance 2, and so on...