This video describes how to treat your instruments in Kontakt as individual instruments in FL Studio. This allows you to have maximum control over your instruments in terms of effects and other features. The process should be fairly similar in any other DAW.
I couldn't find any good tutorials on how to do this nor could I find any good instructions in forums, so I had to go and experiment...so since I figured it out, I'm just sharing it with you so you can have more time to make hot beats!
I used Kontakt 4 and FL Studio 9, so if you have older versions of these programs, the steps might be slightly different.