DanteUruzu,
Your best bet is to set up a Multi (.nkm) that is setup on a per channel basis. Each Staff Represents a Channel, or rather, each Instrument represents a channel. The reason for specifying the latter is that you can have multiple instruments on a staff. To change instruments on a staff select the staff you would like to output through and press "Shift + I". This dialogue will appear:

- Instrument Change.png (27.47 KiB) Viewed 3960 times
You will notice that there is a dropdown menu in the Instrument change dialogue that says "Default Channel" Set the output of the New Instrument (VST>Kontakt>Channel #) by changing the the channel. Set the input of the Kontakt Instrument in the specific Kontakt instance to match the channel you are sending from. You can send 16 Channels out of Notion per Kontakt Staff that you have loaded in the score. Not to fret, you can always add more instruments by adding a second 16 channel Multi to your score.
Your score will look something like this:

- Kontakt 16 Channels.png (41.88 KiB) Viewed 3960 times
In this case, I have added 4 Basic staves to the score. I then set the output of the staves to respond to 4 MIDI Channels of Kontakt. You can locate the channel number at the end of the Instrument names, eg., Kontakt 5 (1). The number in parentheses is the channel number. These names of the instruments can be changed by double clicking the text and renaming the instrument to match the name of the instrument in the Multi.

- Channel Naming.png (536.19 KiB) Viewed 3960 times
In this picture, I have added the Abbey Road Modern Sparkle Kit to the Kontakt Multi. It is outputting from Notion on Channel 1, and to which I always add the Channel information to the name of the instrument. This keeps your channels organized in the score. Repeat the process up to 16 times per Kontakt instance (staves). As long as you have CPU power and RAM, you can add as many instruments as you would like. You will also notice that the drum patch is set to the Kontakt input of MIDI Channel 1.
Each of the instrument changes can be placed anywhere in the score you are working on. They are set chronologically. So, in other words, in the example pictured above, if you want to send to MIDI channel 1 on the first staff in Notion, select the AR Mod Spar. (1) instrument, copy it and place it in the staff.
A really efficient way to work in this manner is to set and save Templates. You can save your Multis (.nkm) anywhere you like on your computer. I always place them in a folder called Kontakt Multis in the same folder that my Notion scores are saved. This way I can always access them again in the future. That way, you do not have to do all of this work over again. You can also make Notion templates to coincide with these setups so that you can always access the entire setup again. Just save it as a Template that you will use in the future and upon opening, perform a Save As...
All Kontakt data is saved in your Notion score on a per score basis. This means that you can save a score and it will retain your Kontakt data for that score. You do not need to save the Kontakt Multi for Notion to access it again in the future, but it is always a good idea, especially if you want to access it again in the future.
I hope this helps,
-Admin