I think it can but I never use it this way. Here's a quick guide:
Inside Kontakt choose New Instrument Bank (from the Diskette menu icon)
The click on the wrench on the Bank Instrument and you'll see a bunch of slots for instruments. Drag .nki instruments into those numbers.
This is the main reason I don't use this method, if you want to setup an instrument you have to load it, set it up (with it's GUI) and then save as it as yet another .nki. Since there is no way to get to the instruments UI from the Instrument Bank.
But lets ignore that. Say you load something into slot 001 and another instrument into slot 002. To test this I recommend loading two vastly different instruments so you can tell. Articulations can be tricky to tell the difference.
On the MIDI track inside SONAR (I almost always use a separate MIDI track not a Instrument track in SONAR) you can insert a bank/patch change (use the Insert Menu item). For the bank/patch change choose "Normal" for the Bank Select Method. Choose 0-bank 0 for the bank. and the Patch you want <unknown> for slot 001 and 1 for slot 002. There may be some way to "teach" SONAR the names of the patches but I'm not sure how.
If you open the event viewer you can see the bank/patch changes
Here's a screenshot which might help (
https://snag.gy/2aW4Nl.jpg for the full sized version)