Okay in the first mission, I went into the backyard and there is an overseer saying his sister isn't a witch. I quickly poison dart the two overseers and they go down, but they also flashed the awareness icon above their heads. Did I get detected? I'm trying to do a ghost run and non-lethal. If so how do I do this without alerting them? Can it even be done? I would assume so since this game seems to think of everything.

Edit
Never mind, I was over thinking it. Just shoot him first and then the next guy.

Equip the sleeping darts, choke the one closest to you and carry the body. Immediately fire the crossbow at the guard facing away from you (not the one facing towards you!) and walk down to the guard and his sister. Afterwards, find a nice place to dump the bodies so rats can't get to them. The rooftop is a nice place, just make sure they don't fall off.

Also, only red bolts count as being detected.

Wait seriously only red bolts? I've been reloading this whole time after one or 2 white ones.

In the "Notes on detection" sticky, it's stated that only Level 4 alert (red bolts) count as actual "detection". Which I.... didn't know also. then

Yeah, I think it's covered pretty clearly in the Arkane post here: http://www.gamesas.com/topic/1415445-notes-on-stealth-detection-chaos-and-trophiesachievements/

(Why that's in the Hardware & Software Issues subforum is beyond me, but it's a very useful post.)