It is possible to set up Kontakt so that several instruments are loaded, each on a different MIDI channel with its own output, here is one way of configuring that in Logic Pro X.
First load one of the multi-output versions of Kontakt on an instrument Track in Logic and then in the track settings, set it to MIDI channel 1 as pictured below:
From the toolbar choose Track>Other>New Track With Next MIDI Channel if you don't see this option, check that the track is set to channel 1 as above, if it is set to All then you won't see this option.
Repeat this step as necessary for the number of instruments you wish to load, instead of selecting from the menu every time you can simply use the key command Control+Enter or Control+Return. You should now see several tracks with the same Instrument number (in this case Inst. 1) each with a different MIDI channel:
At this stage if you know what you intend to load on each MIDI channel, name the tracks to make it easier to identify each, this is a great place to stop and add track icons too if you wish.
Once you have the tracks set up this way, open Kontakt and load the instruments into a multi as shown below with each on a different MIDI Channel:
Now we have each instrument on a different MIDI channel, if you play some MIDI notes on each of the tracks you created you should hear the sounds play back, but currently all of these are playing on the same stereo output.
If you wish to set up separate outputs for each, first make sure the outputs are displayed in Kontakt:
Then from the menu at the top of the outputs choose Batch Functions> Clear Output section and create one individual channel for each loaded instrument as shown below:
Now if you open Logic Pro X's Mixer window (command+2) you can create new Aux tracks as required for each of these outputs by simply clicking on the + icon as shown below:
Now feel free to give these tracks an appropriate name and add them to your arrange Window if you need to.