If you're going for a clean, no kill play through be careful where you place any unconscious bodies you're at fault for. Don't put them where rats may devour them, near bodies of water, or on sloping rooftops where they may make to their death while you're seeing to Granny Rags half an hour later.
Patience, patience, patience! You'll be so very surprised how much doing doing can achieve. It really does pay to wait around in a nice dark corner overseeing things to get a perspective of how things unfold. Guards paths, locations of paths, and animals, things that may even distract the ones you wish to avoids, plan carefully and then tread.
Battering your way through can be achieved also, half of the time, but just makes the path ahead that bit more difficult, with increased awareness, chaos and rats, with less weaponry and resources to rely upon, as well as having to look out for the loot it takes to replace your lost goodies.
Your targets do not always have to assassinated, they can be dealt with in neutral means. The ways to go about finding out these means is usually by eavesdropping and interacting with as many NPCs as possible, and they'll leak useful information that will lead to neutralization... If you have your thinking cap on.