Late to the thread. Good suggestions suicidejunkie -
I wanted watering by hand to really inefficient, to push the player to have a reason for building a water supply - but maybe I went too far.
Also yeah, would make sense to be able to drop water back into a water supply.
The overflow lost-water thing is a bug/oversight - it should automatically fill up any connected water supply containers instead.
And yeah, should probably add some more tool tips and feedback to let the player know what they have to do to grow plants. It's definitely not obvious.