The first Kontakt insert goes to the mixer track that Kontakt is on, the second insert will always go to the one next to it. This will take Kontakt's separate insert outputs and send them to FL's mixer tracks. Go ahead and click that, then Kontakt will disappear and FL greets you with wrapper settings. At the top left you'll see FL Studio's options for the VST, along with a gear icon. Open the Kontakt window (click Kontakt 4 or 5 in the step sequencer). Now it's time to connect Kontakt to FL Studio after adding it as a channel. Now, add Kontakt 4 (or 5) as a channel in FL Studio. If you see three different Kontakt names in red, you done good. Never use this unless you're bored.) Now look at the list again. Click it and hit “Fast Scan” (Scan & Verify is just a dumb thing that separates instruments from effects, it takes a while and throws over 9000 error messages at you. If you don't see it, look for Refresh on the bottom right corner of the list. Check mark it and skip the rest of this section. If you see it (you shouldn't), then great.
“Why isn't FL Studio displaying Kontakt in the channel list?” (if it is, skip this section.) The simple answer is that FL Studio needs to be told to rescan your VST folder in order for it to recognize your new VST's as channels to load. When you first install Kontakt on the path to sampled stardom you may realize that some things aren't going well.