The top row of buttons is where you select the destination channel, these buttons can be automated, with keys of CC controllers. There are two routing modes: single channel is where you redirect midi messages to a channel of choice, in multi channel you can select multiple channels as destination, so you can reprogram a multi instrument setup live.
There are three ways of automation. Use keys, is where you assign keyboard keys as channel switches. You set (manually or by learn button) "start_from" parameter to point to first key number to use, from now on following 16 keys will be used to toggle channels switches. If you don't need to automate all 16 channels, or don't want to trade off so many keys, you can reduce automation range with "size" parameter. You can do the same using CC controllers, "use multi CC" option. Or, if you only use "single channel" destination, you can "use single CC" controller to set destination channel. Automation source can be assigned to any port / any channel, or a specified channel. So you could for example use one controller to play and another controller to select instruments. And this is how it works...
If you'd like to try it, download plain text file, or Kontakt preset file (to place in Kontakt's presets/multiscripts folder). It should work in Kontakt 4.2.4 or newer, I'm not sure about earlier versions. I tested it roughly and it seems to work, but there are no guarantees, so use it at your own risk. Also remember that it is multiscript, you insert it in multi rack, on top of all instruments (use the "scroll" button to activate multiscript rack).