Manually use your workers is absolutely a MUST at the beginning of the game. This way you can make specialised cities, and only build as much farms as needed(the AI tends to overfarm) etc... Later, let's say from the middle ages I automate them, but I keep on eye on them, and quite often corrigate what they are doing, I build more cottages then the AI would do. When I am planning on going state roperty for example I start making workshops and watermills too.