Check your combat settings first, theres an option for non-lethal takedowns which becomes super important for specific encounters. The timing of your melee strikes matters especially against key targets like fezzerk in the blighted village, where you'll need precise non-lethal hits to trigger special dialogue with wyll. When dealing with auntie ethels mind-controlled victims, watch their health bar carefully and switch to non-lethal just before the final blow, this keeps quest options open and prevents accidental kills.

For tougher encounters like recruiting minsc you absolutely need to master the non-lethal timing, as regular kills will lock you out of certain outcomes. The system gets a bit wonky with quest recognition though so save often especially when dealing with important npcs. Keep an eye on your positioning since non-lethal only works in melee range and some enemies have nasty counter-attacks if you miss the timing window. Most regular encounters wont care if you knock them out or kill them but for special cases like guard patrols or vendor confrontations, going non-lethal keeps more doors open later.

After resting enemies you've knocked out usually disappear similar to dead ones, and sometimes dialogue treats them as dead anyway so dont rely too heavily on non-lethal for major story branches. Still worth using when youre unsure about an npcs importance or just roleplaying a merciful character though just remember the mechanics are pretty specific about melee range and timing windows.